Help:Copying FirstGlance Scenes into Proteopedia: Difference between revisions

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<StructureSection size='350' side='right' caption="Selected contacts between an anti-Alzheimer`s drug analog and acetylcholinesterase in [[1gpk]]. Scene generated largely and quite easily in [[FirstGlance in Jmol]]. Atoms shown as balls are within non-covalent bonding distances. Use '''popup''' to see details in this scene!" scene='23/236474/Selected_hup_contacts2/3'>
<StructureSection size='350' side='right' caption="Selected contacts between an anti-Alzheimer`s drug analog and acetylcholinesterase in [[1gpk]]. Scene generated largely and quite easily in [[FirstGlance in Jmol]]. Atoms shown as balls are within non-covalent bonding distances. Use '''popup''' to see details in this scene!" scene='23/236474/Selected_hup_contacts2/3'>
==Procedure==
==Procedure==
''This procedure was improved in July, 2024.''


1. View the molecule in FirstGlance.
1. View the molecule in FirstGlance.
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:*Or, simply go to [http://firstglance.jmol.org firstglance.jmol.org] and enter the PDB code.
:*Or, simply go to [http://firstglance.jmol.org firstglance.jmol.org] and enter the PDB code.
:*If the model does not have a PDB code (e.g. a [[Practical Guide to Homology Modeling|homology model]]), upload the PDB file at [http://firstglance.jmol.org firstglance.jmol.org].
:*If the model does not have a PDB code (e.g. a [[Practical Guide to Homology Modeling|homology model]]), upload the PDB file at [http://firstglance.jmol.org firstglance.jmol.org].
:*If you want to color the protein by evolutionary conservation, there are two methods:
:**It is possible to create a green-linked scene with a molecule colored by evolutionary conservation simply by using the button "evolutionary conservation" in the "color" tab of the [[SAT|Molecular Scene Authoring Tools]]. However, as explained in [[Conservation, Evolutionary#Caveats|Caveats]], this pre-calculated color scheme may obscure important parts of the conservation pattern. This is explained at [[Interpreting_ConSurf_Results#Diversity_in_the_MSA|Diversity in the MSA]] and with an example under [[Interpreting_ConSurf_Results#Average_Pairwise_Distance|Average Pairwise Distance]].
:**You can use custom settings at the ConSurf Server to limit the MSA largely to proteins of a single function. Some examples are explained at [[Interpreting ConSurf Results]], and the basic ConSurf Server procedure is at the [[ConSurf Quick Analysis Procedure]].


2. Use the small link at the bottom "Advanced Options", and on that page check <i>Use the signed Jmol applet</i>.
2. Obtain the '''desired scene''' in FirstGlance in Jmol. Turn off spinning (even if you want it to spin in Proteopedia), and orient and zoom the molecule as you want it to appear initially.
<font color='red'>Using the '''signed applet''' is essential</font>.


3. '''Load''' the appropriate molecule into FirstGlance, giving the signed applet permission to operate. To the lower right of the molecule, instead of seeing <font color='gray'>'''Jmol'''</font>, you should see <font color='red'>'''Jmol_S'''</font>, confirming that the '''signed''' applet is being used.
3. Right-click (Mac: Ctrl-click) on or near the molecule to open JSmol's menu. Select '''File''', '''Save script with state'''. A dialog will appear in which you can choose the location on your computer's disk to save the file. Take note of the name of the file and where you are putting it. This file contains a ''state script'' of JSmol commands that will produce your scene.


4. Obtain the '''desired scene''' in FirstGlance in Jmol. Turn off spinning (even if you want it to spin in Proteopedia), and orient and zoom the molecule as you want it to appear initially.
4. '''Delete the load command.''' Edit the state script file with a [[Help:Plain text editors|plain text editor]]. Before you use the state script, you must the entire command at the end of the 3rd block of commands, and then save the file with that change. Delete <font color="red">everything shown below in red</font>: the entire command beginning with "load", deleting everything up until the closing bracket "}" (keeping that closing bracket!). The load command may be long, wrapping onto several lines in your plain text editor.
 
5. Click on <font color='red'>'''Jmol_S'''</font> to open Jmol's menu. Select '''File''', '''Save script with state'''. A dialog will appear in which you can choose the location on your computer's disk to save the file. Take note of the name of the file and where you are putting it. This file contains a ''state script'' of Jmol commands that will produce your scene.
 
6. '''Comment out the load command.''' Edit the state script file with a [[Help:Plain text editors|plain text editor]]. Before you use the state script, you must insert '''#''' before the word "load" in the command at the end of the 3rd block of commands, and then save the file with that change. This disables the command -- disabling it is crucial. It should look something like this:
<blockquote>
<blockquote>
function _setFileState() {
function _setFileState() {
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<br> &nbsp; <font color="#808080">... blah blah blah ...  </font>
<br> &nbsp; <font color="#808080">... blah blah blah ...  </font>
<br> &nbsp; set smartAromatic true;
<br> &nbsp; set smartAromatic true;
<br> &nbsp; <font color="red">#</font>load /*file*/"<nowiki>http://www.rcsb.org/pdb/cgi/export.cgi/1GPK.pdb.gz</nowiki>";
<br> &nbsp; <font color="red">load /*file*/"<nowiki>http://www.rcsb.org/pdb/cgi/export.cgi/1GPK.pdb.gz</nowiki>"; </font>
<br><br>
<br><br>
}</blockquote>
}</blockquote>


7. Edit the page in Proteopedia where you want to install the scene from FirstGlance in Jmol. Show the '''Scene Authoring Tool'''.
5. Edit the page in Proteopedia where you want to install the scene from FirstGlance in Jmol. Show the '''Scene Authoring Tool'''.
 
6. '''Load your molecule:''' Use the '''load molecule''' tab to load your PDB code (or uploaded molecule) into JSmol in the ''Scene Authoring Tool''.


8. '''Load your molecule:''' Use the '''load molecule''' tab to load your PDB code (or uploaded molecule) into the signed Jmol in the ''Scene Authoring Tool''.
7. '''Exit load molecule mode''' by clicking on, for example, the ''selections'' tab. Additional options will appear below the molecule.


9. '''Drag''' the edited state script file and '''drop''' it into Jmol (where the molecule is displayed). Your scene should appear in a few seconds.
8. '''Drag''' the edited state script file and '''drop''' it into JSmol (where the molecule is displayed). Your scene should appear in a few seconds.


10. Use the '''save scene''' tab to save your scene. Follow the instructions there to insert a green link into the page to show your scene.
9. Use the '''save scene''' tab to save your scene. Follow the instructions there to insert a green link into the page to show your scene.


==Tweaking the Scene from FirstGlance==
==Tweaking the Scene from FirstGlance==
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==See Also==
==See Also==
*[[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link]]
*[[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link]]
*[[Help:How to put a PACUPP scene into Proteopedia]]
*[http://wiki.jmol.org/index.php/Copying_and_pasting_scripts Copying and pasting scripts]
*[http://wiki.jmol.org/index.php/Copying_and_pasting_scripts Copying and pasting scripts]

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Eran Hodis
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