Molecular Playground/Authoring: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 29: | Line 29: | ||
===Facilitate rotation by onlookers=== | ===Facilitate rotation by onlookers=== | ||
MP invites onlookers to interact by rotating the structure at any time. Therefore, scripts should be designed to permit rotation as much of the time as possible. Furthermore, it may be desirable for the | MP invites onlookers to interact by rotating the structure at any time. Therefore, scripts should be designed to permit rotation as much of the time as possible. Furthermore, it may be desirable for the onlooker-set orientation to remain while the script proceeds, perhaps all the way to the end of the script. One command that goes counter to this goal is a ''moveto'' command, which precludes rotation until the specified orientation is completed. In the version of Jmol currently used in Proteopedia (11.8.9 in December, 2009), ''zoomto'' commands also enforce the current orientation, "fighting" with the onlooker who attempts rotation during the timed zoomto. Therefore, the support script provided for MP includes a function ''zoomRotatableTo()'' that performs the zoom while permitting rotation. | ||
===Avoid displays that seriously slow Jmol=== | ===Avoid displays that seriously slow Jmol=== | ||
| Line 65: | Line 65: | ||
There are two ways to prepare the script file. | There are two ways to prepare the script file. | ||
* In Proteopedia, using its [[SAT|Molecular Scene Authoring Tool]]. You don't need to be familiar with Jmol command scripting language. You save the "state script" from Jmol in Proteopedia. | * '''Recommended:''' In Proteopedia, using its [[SAT|Molecular Scene Authoring Tool]]. You don't need to be familiar with Jmol command scripting language. You save the "state script" from Jmol in Proteopedia. | ||
** An '''example''' of a web page created by this method is [[Molecular Playground/Relenza]]. | |||
** '''Instructions for creating your custom scene and saving the state script are in [[Molecular_Playground/Procedures]].''' | ** '''Instructions for creating your custom scene and saving the state script are in [[Molecular_Playground/Procedures]].''' | ||
**''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].''' | **''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].''' | ||
* By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page. See [[#Technical (All Three Levels)]] below for how your script will operate on MP. | |||
* '''For Advanced Jmol Users:''' By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page. See [[#Technical (All Three Levels)]] below for how your script will operate on MP. | |||
===Level II: A Single Molecular Scene With A Color Key=== | ===Level II: A Single Molecular Scene With A Color Key=== | ||
| Line 148: | Line 150: | ||
===Technical (All Three Levels)=== | ===Technical (All Three Levels)=== | ||
MP takes responsibility for loading the PDB file before your script is run, and it adds a delay after your script is run so that your scene will spin for a while before a repeat cycle of your script, or a different script, is run. For all three levels, MP defines the following variables before any master script is run: | |||
* PlaygroundProjection = true; # this if false if undefined | |||
* PlaygroundContentPath # the path on the MP server to your .spt and .pdb files. The filename must be appended to this. | |||
* PlaygroundSupportScriptPath # the path on the MP server to MPSupportVersion01.spt and MPSceneVersion01.spt. The filename must be appended. | |||
<!-- Adam plans in April 2011 that these will become: | |||
PlaygroundModelPath | |||
PlaygroundScriptPath | |||
PlaygroundSupportPath | |||
--> | |||
==Web Pages== | ==Web Pages== | ||
| Line 203: | Line 216: | ||
==Notes and References== | ==Notes and References== | ||
<references /> | <references /> | ||
==See Also== | |||
* [[Molecular Playground]] | |||
* [[CBI Molecules]] | |||
[[Category: Molecular Playground]] | [[Category: Molecular Playground]] | ||