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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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. | 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. ''' | 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. | ||
<blockquote> | <blockquote> | ||
function _setFileState() { | function _setFileState() { | ||
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<br> <font color="#808080">... blah blah blah ... </font> | <br> <font color="#808080">... blah blah blah ... </font> | ||
<br> set smartAromatic true; | <br> set smartAromatic true; | ||
<br> <font color="red" | <br> <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> | ||
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6. '''Load your molecule:''' Use the '''load molecule''' tab to load your PDB code (or uploaded molecule) into JSmol in 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''. | ||
7. ''' | 7. '''Exit load molecule mode''' by clicking on, for example, the ''selections'' tab. Additional options will appear below the molecule. | ||
8. 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. | 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. | ||
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== | ||