Secondary structure: Difference between revisions

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==How Jmol Determines Secondary Structure==

===From PDB files===

[[PDB files]] usually contain HELIX and SHEET records, in their headers. These represent the authors' determinations, and when present, [[Jmol]] obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix.

[[PDB files]] usually contain HELIX and SHEET records, in their headers. (Many PDB files used to contain TURN records, but in revision 3.2 of the [[PDB files|PDB data format]], TURN records were abolished.) These represent the authors' determinations, and when present, [[Jmol]] obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix.

Jmol's standard color scheme for secondary structure (see [[Help:Color_Keys]]):

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===Jmol's objective calculation===

When the PDB file lacks HELIX and SHEET records ~~(Many PDB files used to contain TURN records, but in revision 3.2 of the [[PDB files|PDB data format]], TURN records were abolished.)~~, Jmol will determine secondary structure using objective criteria. Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. '[[Calculate structure]]' is the Jmol command which does this re-determination. ~~Several other commands are~~ required to display the ''Secondary Structure'' color scheme and hydrogen bonds contained in the secondary structures. ~~The~~ script is 'select protein; calculate structure; cartoon; color structure; calculate hbonds ~~structure~~'.

When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria. Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. '[[Calculate structure]]' is the Jmol command which does this re-determination. The complete script required to display the ''Secondary Structure'' color scheme and hydrogen bonds (hbonds) contained in the secondary structures is 'select protein; calculate structure; cartoon; color structure; calculate hbonds structure'. At the present time 'calculate hbonds structure' messes up the post-processing by Proteopedia, and any scene whose script contains this command is not displayed. The above scenes which colors the helices, sheets and turns without displaying the hbonds were constructed using only 'select protein; calculate structure; cartoon; color structure'. If 'calculate hbonds strucutre' is run through the Jmol console as described below, the hbonds in these three types of structures will be displayed.

~~If a Proteopedia page does not contain this more detailed ''Secondary Structure'' information, it~~ can be displayed by clicking on the ''Jmol frank'' which opens the ''main menu'', clicking on ''Console'', in the bottom console box entering the script:

Hbonds in secondary structures can be displayed by clicking on the ''Jmol frank'' which opens the ''main menu'', clicking on ''Console'', in the bottom console box entering the command: calculate hbonds structure

select protein; calculate structure; cartoon; color structure; calculate hbonds structure

and then clicking ''Run''.</blockquote>

~~and then clicking ''Run''. See also [[Calculate structure]]~~.

If a Proteopedia page does not contain the more detailed ''Secondary Structure'' information, it can be displayed by running the script:

select protein; calculate structure; cartoon; color structure; calculate hbonds structure in the Jmol console as described above.

</blockquote>

See [[Calculate structure]] for more details.

===Examples===

If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the sheets and the '''alpha helices''' being displayed the '''310 helices''' and different types of turns in blue are also shown. If the above series of commands are applied when the structure of glycogen phosphorylase (domain 2) is displayed above, all four chains will be initially displayed, but clicking the ''domain 2 of glycogen phosphorylase'' green link (above) will display only domain 2 of chain A. You will observe all three types of helices, and the turns will be colored blue. More detail on how calculate structure determines helices, strands and turns is at [[Calculate structure]].

Secondary structure: Difference between revisions

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@@ Line 16: / Line 16: @@
 ==How Jmol Determines Secondary Structure==
 ===From PDB files===
-[[PDB files]] usually contain HELIX and SHEET records, in their headers. These represent the authors' determinations, and when present, [[Jmol]] obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix.
+[[PDB files]] usually contain HELIX and SHEET records, in their headers. (Many PDB files used to contain TURN records, but in revision 3.2 of the  [[PDB files|PDB data format]], TURN records were abolished.) These represent the authors' determinations, and when present, [[Jmol]] obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix.
 Jmol's standard color scheme for secondary structure (see [[Help:Color_Keys]]):
@@ Line 28: / Line 28: @@
 ===Jmol's objective calculation===
-When the PDB file lacks HELIX and SHEET records (Many PDB files used to contain TURN records, but in revision 3.2 of the  [[PDB files|PDB data format]], TURN records were abolished.), Jmol will determine secondary structure using objective criteria. Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. '[[Calculate structure]]' is the Jmol command which does this re-determination. Several other commands are required to display the ''Secondary Structure'' color scheme and hydrogen bonds contained in the secondary structures. The script is 'select protein; calculate structure; cartoon; color structure; calculate hbonds structure'.
+When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria. Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. '[[Calculate structure]]' is the Jmol command which does this re-determination. The complete script required to display the ''Secondary Structure'' color scheme and hydrogen bonds (hbonds) contained in the secondary structures is 'select protein; calculate structure; cartoon; color structure; calculate hbonds structure'. At the present time 'calculate hbonds structure' messes up the post-processing by Proteopedia, and any scene whose script contains this command is not displayed. The above scenes which colors the helices, sheets and turns without displaying the hbonds were constructed using only 'select protein; calculate structure; cartoon; color structure'. If 'calculate hbonds strucutre' is run through the Jmol console as described below, the hbonds in these three types of structures will be displayed.
 <blockquote>
-If a Proteopedia page does not contain this more detailed ''Secondary Structure'' information, it can be displayed by clicking on the ''Jmol frank'' which opens the ''main menu'', clicking on ''Console'', in the bottom console box entering the script:
+Hbonds in secondary structures can be displayed by clicking on the ''Jmol frank'' which opens the ''main menu'', clicking on ''Console'', in the bottom console box entering the command: <span style='background-color:yellow;'>calculate hbonds structure</span>
-<span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span>
+and then clicking ''Run''.</blockquote>
-and then clicking ''Run''. See also [[Calculate structure]].
+<blockquote>
+If a Proteopedia page does not contain the more detailed ''Secondary Structure'' information, it can be displayed by running the script:
+<span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span> in the Jmol console as described above.
 </blockquote>
+See [[Calculate structure]] for more details.
 ===Examples===
 If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the sheets and the <font color=#FF0080>'''alpha helices'''</font> being displayed the <font color=#A00080>'''3<sub>10</sub> helices'''</font> and different types of turns in blue are also shown. If the above series of commands are applied when the structure of glycogen phosphorylase (domain 2) is displayed above, all four chains will be initially displayed, but clicking the ''domain 2 of glycogen phosphorylase'' green link (above) will display only domain 2 of chain A. You will observe all three types of helices, and the turns will be colored blue. More detail on how calculate structure determines helices, strands and turns is at [[Calculate structure]].