https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Shari+DunhamProteopedia - User contributions [en]2026-10-03T09:12:30ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Shari_Dunham/Peptide1&diff=2954895Shari Dunham/Peptide12018-10-08T10:01:31Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Peptide 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
Ball and stick representations: <scene name='79/796888/Peptide-1-ball-and-stick/2'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/3'>with protein backbone only</scene><br />
<br />
Space fill representations: <scene name='79/796888/Peptide-1-ball-and-stick/4'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/5'>with protein backbone only</scene> <br />
<br />
Ribbon representation: <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>with protein backbone only</scene><br />
<br />
== Displaying Hydrogen Bonds ==<br />
Let's view the hydrogen bonds that can be calculated from optimal distances/angles in this structure: for the structure <scene name='79/796888/Peptide-1-ball-and-stick/7'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/8'>with protein backbone only</scene>. Use one of these representations to measure the distances necessary to complete the table in your activity.<br />
<br />
== A Reminder on Measuring Distances Between Atoms ==<br />
*You might want to toggle off the spinning of the molecule (see spin button in lower left corner of the structure box).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954894Sandbox 17422018-10-08T09:59:38Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Peptide 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
Ball and stick representations: <scene name='79/796888/Peptide-1-ball-and-stick/2'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/3'>with protein backbone only</scene><br />
<br />
Space fill representations: <scene name='79/796888/Peptide-1-ball-and-stick/4'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/5'>with protein backbone only</scene> <br />
<br />
Ribbon representation: <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>with protein backbone only</scene><br />
<br />
== Displaying Hydrogen Bonds ==<br />
Let's view the hydrogen bonds that can be calculated from optimal distances/angles in this structure: for the structure <scene name='79/796888/Peptide-1-ball-and-stick/7'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/8'>with protein backbone only</scene>. Use one of these representations to measure the distances necessary to complete the table in your activity.<br />
<br />
== A Reminder on Measuring Distances Between Atoms ==<br />
*You might want to toggle off the spinning of the molecule (see spin button in lower left corner of the structure box).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954893Sandbox 17422018-10-08T09:57:51Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Peptide 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
Ball and stick representations: <scene name='79/796888/Peptide-1-ball-and-stick/2'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/3'>with protein backbone only</scene><br />
<br />
Space fill representations: <scene name='79/796888/Peptide-1-ball-and-stick/4'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/5'>with protein backbone only</scene> <br />
<br />
Ribbon representation: <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>with protein backbone only</scene><br />
<br />
== Displaying Hydrogen Bonds ==<br />
Let's view the hydrogen bonds that can be calculated from optimal distances/angles in this structure: for the structure <scene name='79/796888/Peptide-1-ball-and-stick/7'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/8'>with protein backbone only</scene>. Use one of these representations to measure the distances necessary to complete the table in your activity.<br />
<br />
== A Reminder on Measuring Distances Between Atoms ==<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954892Sandbox 17422018-10-08T09:54:33Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Peptide 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
Ball and stick representations: <scene name='79/796888/Peptide-1-ball-and-stick/2'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/3'>with protein backbone only</scene><br />
<br />
Space fill representations: <scene name='79/796888/Peptide-1-ball-and-stick/4'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/5'>with protein backbone only</scene> <br />
<br />
Ribbon representation: <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>with protein backbone only</scene><br />
<br />
== Displaying Hydrogen Bonds ==<br />
Let's view the hydrogen bonds that can be calculated from optimal distances/angles in this structure: for the structure with side chains, or with protein backbone only. Use one of these representations to measure the distances necessary to complete the table in your activity.<br />
<br />
== A Reminder on Measuring Distances Between Atoms ==<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954891Sandbox 17422018-10-08T09:50:31Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Peptide 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
Ball and stick representations: <scene name='79/796888/Peptide-1-ball-and-stick/2'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/3'>with protein backbone only</scene><br />
<br />
Space fill representations: <scene name='79/796888/Peptide-1-ball-and-stick/4'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/5'>with protein backbone only</scene> <br />
<br />
Ribbon representation: <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>with protein backbone only</scene><br />
<br />
== Displaying Hydrogen Bonds ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
== Measuring Distances Between Atoms ==<br />
<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Shari_Dunham/Peptide1&diff=2954890Shari Dunham/Peptide12018-10-08T02:07:33Z<p>Shari Dunham: New page: ==Protein Secondary Structure Activity: Peptide 1== <StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'>...</p>
<hr />
<div>==Protein Secondary Structure Activity: Peptide 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
<scene name='79/796888/Peptide-1-ball-and-stick/2'>Ball-and-stick</scene> is the same as the default representation above, but just an end-on orientation of the peptide.<br />
<br />
<scene name='79/796888/Peptide-1-backbone-b-and-s/2'>Protein backbone</scene> is another representation that is useful for viewing just the backbone atoms of peptides and proteins.<br />
<br />
The <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation more accurately represents the space occupied by the electron cloud of each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.<br />
<br />
A <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>ribbon</scene> representation is a more simplified rendering that is often used to trace the backbone location in large protein structures.<br />
<br />
== Displaying Hydrogen Bonds ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
== Measuring Distances Between Atoms ==<br />
<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954889Sandbox 17422018-10-08T02:03:25Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Peptide 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
<scene name='79/796888/Peptide-1-ball-and-stick/2'>Ball-and-stick</scene> is the same as the default representation above, but just an end-on orientation of the peptide.<br />
<br />
<scene name='79/796888/Peptide-1-backbone-b-and-s/2'>Protein backbone</scene> is another representation that is useful for viewing just the backbone atoms of peptides and proteins.<br />
<br />
The <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation more accurately represents the space occupied by the electron cloud of each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.<br />
<br />
A <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>ribbon</scene> representation is a more simplified rendering that is often used to trace the backbone location in large protein structures.<br />
<br />
== Displaying Hydrogen Bonds ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
== Measuring Distances Between Atoms ==<br />
<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954888Sandbox 17422018-10-08T02:02:25Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
<scene name='79/796888/Peptide-1-ball-and-stick/2'>Ball-and-stick</scene> is the same as the default representation above, but just an end-on orientation of the peptide.<br />
<br />
<scene name='79/796888/Peptide-1-backbone-b-and-s/2'>Protein backbone</scene> is another representation that is useful for viewing just the backbone atoms of peptides and proteins.<br />
<br />
The <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation more accurately represents the space occupied by the electron cloud of each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.<br />
<br />
A <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>ribbon</scene> representation is a more simplified rendering that is often used to trace the backbone location in large protein structures.<br />
<br />
== Displaying Hydrogen Bonds ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
== Measuring Distances Between Atoms ==<br />
<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954887Sandbox 17422018-10-08T01:45:11Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
<scene name='79/796888/Peptide-1-ball-and-stick/2'>Ball-and-stick</scene> is the same as the default representation above, but just an end-on orientation of the peptide.<br />
<br />
<scene name='79/796888/Peptide-1-backbone-b-and-s/2'>Protein backbone</scene> is another representation that is useful for viewing just the backbone atoms of peptides and proteins.<br />
<br />
The <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation more accurately represents the space occupied by the electron cloud of each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.<br />
<br />
A <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>ribbon</scene> representation is a more simplified rendering that is often used to trace the backbone location in large protein structures.<br />
<br />
== Displaying Hydrogen Bonds ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954886Sandbox 17422018-10-08T01:44:26Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
scene name='79/796888/Peptide-1-ball-and-stick/2'>"Ball-and-stick"</scene> is the same as the default representation above, but just an end-on orientation of the peptide.<br />
<br />
<scene name='79/796888/Peptide-1-backbone-b-and-s/2'>Protein backbone</scene> is another representation that is useful for viewing just the backbone atoms of peptides and proteins.<br />
<br />
The <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation more accurately represents the space occupied by the electron cloud of each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.<br />
<br />
A <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>ribbon</scene> representation is a more simplified rendering that is often used to trace the backbone location in large protein structures.<br />
<br />
== Displaying Hydrogen Bonds ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954885Sandbox 17422018-10-08T00:58:58Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
Peptide 1 is an 11-amino acid fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/796888/Peptide-1-ball-and-stick/2'>"ball-and-stick"</scene>. This is an end-on orientation of the peptide.<br />
<br />
Another representation that is useful for viewing peptides includes only the <scene name='79/796888/Peptide-1-backbone-b-and-s/2'>protein backbone</scene>.<br />
<br />
If you use a <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation, it more accurately represents the space occupied by each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.<br />
<br />
A more simplified rendering is called <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>ribbon</scene> and is often used to trace the backbone location in large protein structures.<br />
<br />
== Displaying Hydrogen Bonds ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954884Sandbox 17422018-10-08T00:56:24Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
Peptide 1 is an 11-amino acid fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/796888/Peptide-1-ball-and-stick/2'>"ball-and-stick"</scene>. This is an end-on orientation of the peptide.<br />
<br />
Another representation that is useful for viewing peptides includes only the <scene name='79/796888/Peptide-1-backbone-b-and-s/2'>protein backbone</scene>.<br />
<br />
If you use a <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation, it more accurately represents the space occupied by each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.<br />
<br />
A more simplified rendering is called <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>ribbon</scene> and is often used for large protein structures.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954883Sandbox 17422018-10-08T00:53:34Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
Peptide 1 is an 11-amino acid fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/796888/Peptide-1-ball-and-stick/2'>"ball-and-stick"</scene>. This is an end-on orientation of the peptide.<br />
<br />
Another representation that is useful for viewing peptides includes only the <scene name='79/796888/Peptide-1-backbone-b-and-s/2'>protein backbone</scene>.<br />
<br />
If you use a <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation, it more accurately represents the space occupied by each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone from an end-on orientation.<br />
<br />
A more simplified rendering is called <scene name='79/796888/Peptide-1-backbone-b-and-s/4'>cartoon</scene> and is often used for large protein structures.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954882Sandbox 17422018-10-08T00:41:08Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
Peptide 1 is an 11-amino acid fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/796888/Peptide-1-ball-and-stick/2'>"ball-and-stick"</scene>. This is an end-on orientation of the peptide.<br />
<br />
Another representation that is useful for viewing peptides includes only the <scene name='79/796888/Peptide-1-backbone-b-and-s/2'>protein backbone</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
</StructureSection><br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Model 2' scene='<scene name='79/796888/Peptide-1-ball-and-stick/1'></scene>'><br />
This structure file in Model 2 represents five water molecules in the liquid state. Use the green links in the text below to view different representations of these water molecules and to help you answer the questions in your Activity #1 handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/795974/Ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954881Sandbox 17422018-10-08T00:36:23Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
Peptide 1 is an 11-amino acid fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/796888/Peptide-1-ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another representation that is useful for viewing peptides includes only the <scene name='79/796888/Peptide-1-backbone-b-and-s/1'>protein backbone</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
</StructureSection><br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Model 2' scene='<scene name='79/796888/Peptide-1-ball-and-stick/1'></scene>'><br />
This structure file in Model 2 represents five water molecules in the liquid state. Use the green links in the text below to view different representations of these water molecules and to help you answer the questions in your Activity #1 handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/795974/Ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954880Sandbox 17422018-10-08T00:33:44Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
Peptide 1 is an 11-amino acid fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/795974/Ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
</StructureSection><br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Model 2' scene='<scene name='79/796888/Peptide-1-ball-and-stick/1'></scene>'><br />
This structure file in Model 2 represents five water molecules in the liquid state. Use the green links in the text below to view different representations of these water molecules and to help you answer the questions in your Activity #1 handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/795974/Ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954879Sandbox 17422018-10-08T00:32:05Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'><br />
<br />
<br />
</StructureSection><br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Model 2' scene='<scene name='79/796888/Peptide-1-ball-and-stick/1'></scene>'><br />
This structure file in Model 2 represents five water molecules in the liquid state. Use the green links in the text below to view different representations of these water molecules and to help you answer the questions in your Activity #1 handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/795974/Ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954878Sandbox 17422018-10-08T00:30:29Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Model 1==<br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1''><br />
<br />
</StructureSection><br />
<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Model 2' scene='<scene name='79/796888/Peptide-1-ball-and-stick/1'></scene>'><br />
This structure file in Model 2 represents five water molecules in the liquid state. Use the green links in the text below to view different representations of these water molecules and to help you answer the questions in your Activity #1 handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/795974/Ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954877Sandbox 17422018-10-08T00:26:42Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure: Model 1==<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Model 2' scene='<scene name='79/796888/Peptide-1-ball-and-stick/1'></scene>'><br />
This structure file in Model 2 represents five water molecules in the liquid state. Use the green links in the text below to view different representations of these water molecules and to help you answer the questions in your Activity #1 handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/795974/Ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954876Sandbox 17422018-10-08T00:23:13Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure: Model 1==<br />
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Model 1' scene='<scene name='79/796888/Peptide-1-ball-and-stick/1'>Peptide-1</scene>'><br />
This structure represents an 11-amino acid peptide from the middle of a protein. Use the green links in the text below to view different representations of this peptide and to help you answer the questions in your activity handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/796888/Peptide-1-ball-and-stick/1'>Peptide-1</scene>'> and contains all of the heteroatoms in the structure.<br />
<br />
Another view that may be useful it to view the ball-and-stick version of the structure with just the <scene name='79/796888/Peptide-1-backbone-b-and-s/1'>backbone atoms</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2954875Sandbox 17422018-10-08T00:09:24Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Pre-Class Peptide==<br />
<StructureSection load='Dunham-Pre-class-peptide-1.pdb' size='580' side='right' caption='Peptide-1' scene='<scene name='<scene name='79/796888/Peptide-1-ball-and-stick/1'>Peptide-1</scene>'><br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Shari_Dunham/Pre-class-peptide&diff=2953608Shari Dunham/Pre-class-peptide2018-10-03T08:11:30Z<p>Shari Dunham: New page: ==Protein Secondary Structure Activity: Pre-Class Peptide== <StructureSection load='Dunham-Pre-class-peptide-1.pdb' size='580' side='right' caption='Pre-class peptide' scene='79/796888/Pre...</p>
<hr />
<div>==Protein Secondary Structure Activity: Pre-Class Peptide==<br />
<StructureSection load='Dunham-Pre-class-peptide-1.pdb' size='580' side='right' caption='Pre-class peptide' scene='79/796888/Pre-class-peptide-1-scene1/1'><br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2953604Sandbox 17422018-10-03T08:09:17Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Pre-Class Peptide==<br />
<StructureSection load='Dunham-Pre-class-peptide-1.pdb' size='580' side='right' caption='Pre-class peptide' scene='79/796888/Pre-class-peptide-1-scene1/1'><br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2953603Sandbox 17422018-10-03T07:59:50Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Pre-Class Peptide==<br />
<StructureSection load='Dunham-Pre-class-peptide-1.pdb' size='580' side='right' caption='Model 2' scene=''><br />
This structure represents the peptide in the pre-class questions for our next class.<br />
<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2953532Sandbox 17422018-10-03T07:54:03Z<p>Shari Dunham: </p>
<hr />
<div>==Protein Secondary Structure Activity: Pre-Class Peptide==<br />
<StructureSection load='Dunham-Pre-class-peptide-1.pdb' size='580' side='right' caption='Model 2' scene=''><br />
This structure file in Model 2 represents five water molecules in the liquid state. Use the green links in the text below to view different representations of these water molecules and to help you answer the questions in your Activity #1 handout.<br />
<br />
== Representations==<br />
The default representation is called <scene name='79/795974/Ball-and-stick/1'>"ball-and-stick"</scene>.<br />
<br />
Another very common representation is known as "spacefill". Explore the different levels of "spacefill" for these molecules including:<scene name='79/795974/Spacefill_20/1'>spacefill 20%</scene>, <scene name='79/795974/Spacefill_50/1'>spacefill 50%</scene>, and <scene name='79/795974/Spacefill_100/1'>spacefill 100%</scene>.<br />
<br />
== Measuring Distances Between Atoms ==<br />
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.<br />
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:<br />
<br />
*You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).<br />
*Put your cursor in the structure window.<br />
*Decide on two atoms for which you would like to measure the distance between them.<br />
*Using your cursor, hover over one atom and double-click on that first atom.<br />
*Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.<br />
<br />
*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.<br />
<br />
== Measuring Angles formed by 3 Atoms ==<br />
To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:<br />
<br />
*Stop the spinning of the Model.<br />
*Hover your cursor over the first atom and double-click on that atom.<br />
*Single-click on the second atom (the middle one).<br />
*Finish by double-clicking on the third atom. An angle label should now appear on the structure.<br />
<br />
</StructureSection></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Shari_Dunham/FourAAs&diff=2947242Shari Dunham/FourAAs2018-09-17T12:32:36Z<p>Shari Dunham: New page: ==Amino Acid Preclass Activity: Model 1B== Alanine (left) and Glycine (right) <StructureSection load='Ala.pdb' size='250' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'> <S...</p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
Alanine (left) and Glycine (right)<br />
<StructureSection load='Ala.pdb' size='250' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='250' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
Glutamate (left) and Tyrosine (right)<br />
<StructureSection load='Glutamate.pdb' size='250' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='250' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
</StructureSection><br />
====</div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947241Sandbox 17422018-09-17T12:31:41Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
Alanine (left) and Glycine (right)<br />
<StructureSection load='Ala.pdb' size='250' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='250' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
Glutamate (left) and Tyrosine (right)<br />
<StructureSection load='Glutamate.pdb' size='250' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='250' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
</StructureSection><br />
====</div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947240Sandbox 17422018-09-17T12:28:19Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
Alanine (left) and Glycine (right)<br />
<StructureSection load='Ala.pdb' size='250' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='250' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
Glutamate (left) and Tyrosine (right)<br />
<StructureSection load='Glutamate.pdb' size='250' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='250' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947239Sandbox 17422018-09-17T12:26:32Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<br />
<StructureSection load='Ala.pdb' size='250' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='250' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
Alanine (left) and Glycine (right)<br />
<br />
</StructureSection><br />
====<br />
<br />
<StructureSection load='Glutamate.pdb' size='250' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='250' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
Glutamate (left) and Tyrosine (right)<br />
<br />
</StructureSection><br />
====<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947238Sandbox 17422018-09-17T12:24:53Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='250' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='250' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<StructureSection load='Glutamate.pdb' size='250' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='250' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947237Sandbox 17422018-09-17T12:24:06Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='300' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'>A<br />
<StructureSection load='Dunham_Glycine.pdb' size='300' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<StructureSection load='Glutamate.pdb' size='300' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='300' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947236Sandbox 17422018-09-17T12:23:09Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='300' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<StructureSection load='Dunham_Glycine.pdb' size='300' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<br />
</StructureSection><br />
====<br />
<br />
<StructureSection load='Glutamate.pdb' size='300' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='300' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
</StructureSection><br />
====<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947235Sandbox 17422018-09-17T12:22:06Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='400' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='400' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<StructureSection load='Glutamate.pdb' size='400' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='400' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947234Sandbox 17422018-09-17T12:21:28Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='220' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='200' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<StructureSection load='Glutamate.pdb' size='220' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='220' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947233Sandbox 17422018-09-17T12:20:17Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='220' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='200' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
</StructureSection><br />
====<br />
<br />
<StructureSection load='Glutamate.pdb' size='220' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='220' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
<br />
<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947232Sandbox 17422018-09-17T12:18:25Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='220' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='200' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
== Disease ==<br />
<br />
<StructureSection load='Glutamate.pdb' size='220' side='left' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_Tyrosine.pdb' size='220' side='right' caption='Tyrosine' scene='79/796888/Tyr_scene_1/1'><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
<br />
<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947231Sandbox 17422018-09-17T12:16:05Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='220' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Dunham_Glycine.pdb' size='200' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
<Structure load='Glutamate.pdb' size='220' side='center' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<br />
== Disease ==<br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
<br />
<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947230Sandbox 17422018-09-17T12:14:41Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='220' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Glutamate.pdb' size='220' side='center' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<Structure load='Dunham_Glycine.pdb' size='200' frame='true' align='left' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947229Sandbox 17422018-09-17T12:11:46Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Ala.pdb' size='220' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<StructureSection load='Glutamate.pdb' size='220' side='center' caption='Glutamine' scene='79/796888/Glu_scene_1/2'><br />
<StructureSection load='Dunham_glycine.pdb' size='220' side='right' caption='Glycine' scene='79/796888/Gly_scene_1/1'><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947228Sandbox 17422018-09-17T11:59:05Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Waters-5c.pdb' size='220' side='left' caption='Alanine' scene='79/796888/Ala_secne_1/1'><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947227Sandbox 17422018-09-17T11:58:10Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Waters-5c.pdb' size='220' side='left' caption='Model 2' scene='79/796888/Ala_secne_1/1'><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947226Sandbox 17422018-09-17T11:51:46Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1B==<br />
<br />
<StructureSection load='Waters-5c.pdb' size='220' side='left' caption='Model 2' scene='79/796888/Ala_secne_1/1'><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947225Sandbox 17422018-09-17T11:46:46Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1==<br />
<br />
<Structure load='Ala' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
<scene name='79/796888/Tyr_scene_1/1'>Tyrosine</scene><br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=File:Dunham_Tyrosine.pdb&diff=2947218File:Dunham Tyrosine.pdb2018-09-17T08:26:55Z<p>Shari Dunham: </p>
<hr />
<div></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947217Sandbox 17422018-09-17T08:26:10Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1==<br />
<br />
<Structure load='Ala' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
<scene name='79/796888/Glu_scene_1/2'>Glutamate</scene><br />
<scene name='79/796888/Gly_scene_1/1'>Glycine</scene><br />
Tyrosine<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=Sandbox_1742&diff=2947216Sandbox 17422018-09-17T08:22:59Z<p>Shari Dunham: </p>
<hr />
<div>==Amino Acid Preclass Activity: Model 1==<br />
<br />
<Structure load='Ala' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
<br />
This is a default text for your page '''Sandbox 1742'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='79/796888/Ala_secne_1/1'>Alanine</scene><br />
Glutamate<br />
Glycine<br />
Tyrosine<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Shari Dunhamhttps://proteopedia.org/index.php?title=File:Dunham_Glycine.pdb&diff=2947215File:Dunham Glycine.pdb2018-09-17T08:20:47Z<p>Shari Dunham: </p>
<hr />
<div></div>Shari Dunhamhttps://proteopedia.org/index.php?title=File:Alanine.pdb&diff=2947205File:Alanine.pdb2018-09-16T19:45:26Z<p>Shari Dunham: uploaded a new version of "Image:Alanine.pdb"</p>
<hr />
<div></div>Shari Dunhamhttps://proteopedia.org/index.php?title=File:Dunham-Ala.pdb&diff=2947204File:Dunham-Ala.pdb2018-09-16T19:43:39Z<p>Shari Dunham: </p>
<hr />
<div></div>Shari Dunhamhttps://proteopedia.org/index.php?title=File:Dunham-B-D-Glc.pdb&diff=2947192File:Dunham-B-D-Glc.pdb2018-09-16T19:11:34Z<p>Shari Dunham: This is a structure of beta-D-glucopyranose downloaded from Klothos.</p>
<hr />
<div>This is a structure of beta-D-glucopyranose downloaded from Klothos.</div>Shari Dunham