Scene authoring tools: Difference between revisions

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[[Image:SAT show.JPG|350px]]

The ''Scene authoring tools'' are accessible when you are editing a page. Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box where all the wikitext of the page lives--here you can change the text of the page. If you scroll down some, near the bottom, you'll find in bold letters '''SAT (Scene authoring tools) [show]'''. Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not contain a Jmol window yet (~~not~~ <Structure> or <StructureSection> tags), ~~there~~ will be access to the SAT. In this case, first edit the page to include ~~one~~ (using the [[Image:Structure buttons.JPG|50px]] buttons above the text-editing area), save and then edit again to see the link to the SAT. New pages have placeholder content that includes these tags, but this page for example does not.

The ''Scene authoring tools'' are accessible when you are editing a page. Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box where all the wikitext of the page lives--here you can change the text of the page. If you scroll down some, near the bottom, you'll find in bold letters '''SAT (Scene authoring tools) [show]'''. Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not contain a Jmol window yet (no <Structure> or <StructureSection> tags), the page will lack access to the SAT. In this case, first edit the page to include a Jmol window (using the [[Image:Structure buttons.JPG|50px]] buttons above the text-editing area), save and then edit again to see the link to the SAT. New pages have placeholder content that includes these tags, but this page for example does not.

<!--

<!--<Structure load='

----

Insert PDB code or filename here' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

A short and rough, temporary video tutorial can be viewed here: http://www.weizmann.ac.il/ISPC/Proteopedia.html.

-->

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To load a file that has a PDB ID, input the ID into the first input area and click the load button. The file will be fetched from the PDB database.

To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Special:Upload]] (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia). Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia ~~upladed~~ file" and click load.

To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Special:Upload]] (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia). Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia uploaded file" and click load.

Uploaded file can have various formats recognized by Jmol's "load" command. For example, you can load a .PNGJ file to load coordinates and a 3D scene in one step.

There is a checkbox to add calculated positions of hydrogen atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.

There is a checkbox to add calculated positions of '''hydrogen''' atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.

Another optional field allows to enter instructions that will be used to '''filter''' which atoms of the original model will be either loaded or ignored.

For example, to load just the alpha carbons, to exclude water, include or exclude other hetero groups (ligands), load a specified biomolecule (biological unit), etc. See [[Biological Unit: Showing]] for instructions.

You can also check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).

=='load scene' tab==

Scene authoring tools: Difference between revisions

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 [[Image:SAT show.JPG|350px]]
-The ''Scene authoring tools'' are accessible when you are editing a page.  Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box where all the wikitext of the page lives--here you can change the text of the page.  If you scroll down some, near the bottom, you'll find in bold letters '''SAT (Scene authoring tools) [show]'''.  Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not contain a Jmol window yet (not &lt;Structure&gt; or &lt;StructureSection&gt; tags), there will be access to the SAT. In this case, first edit the page to include one (using the [[Image:Structure buttons.JPG|50px]] buttons above the text-editing area), save and then edit again to see the link to the SAT. New pages have placeholder content that includes these tags, but this page for example does not.
+The ''Scene authoring tools'' are accessible when you are editing a page.  Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box where all the wikitext of the page lives--here you can change the text of the page.  If you scroll down some, near the bottom, you'll find in bold letters '''SAT (Scene authoring tools) [show]'''.  Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not contain a Jmol window yet (no &lt;Structure&gt; or &lt;StructureSection&gt; tags), the page will lack access to the SAT. In this case, first edit the page to include a Jmol window (using the [[Image:Structure buttons.JPG|50px]] buttons above the text-editing area), save and then edit again to see the link to the SAT. New pages have placeholder content that includes these tags, but this page for example does not.
-<!--
+<!--<Structure load='
+----
+Insert PDB code or filename here' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
 A short and rough, temporary video tutorial can be viewed here: http://www.weizmann.ac.il/ISPC/Proteopedia.html.
 -->
@@ Line 36: / Line 38: @@
 To load a file that has a PDB ID, input the ID into the first input area and click the load button.  The file will be fetched from the PDB database.
-To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Special:Upload]] (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia).  Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia upladed file" and click load.
+To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Special:Upload]] (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia).  Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia uploaded file" and click load.
 Uploaded file can have various formats recognized by Jmol's "load" command. For example, you can load a .PNGJ file to load coordinates and a 3D scene in one step.
-There is a checkbox to add calculated positions of hydrogen atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.
+There is a checkbox to add calculated positions of '''hydrogen''' atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.
+Another optional field allows to enter instructions that will be used to '''filter''' which atoms of the original model will be either loaded or ignored.
+For example, to load just the alpha carbons, to exclude water, include or exclude other hetero groups (ligands), load a specified biomolecule (biological unit), etc. See [[Biological Unit: Showing]] for instructions.
+You can also check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).
 =='load scene' tab==