User:Tom Gluick/glutamine synthetase: Difference between revisions

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If you scroll up to the original JMOL applet, and click on ADP, you will notice that the image fades allowing the ligand to become prominent as it zooms in and out while the image spins. ~~First I dare~~ you to ~~try~~ to ~~do this using~~ the ~~Screen~~ Authoring Tools; <applet load='2qc8' size='300' frame='true' align='right' caption='JMOL Console Practice Applet' /~~> This is <scene name='User:Tom_Gluick/glutamine_synthetase/Sat_adp_transparent/1'>My attempt</scene~~>. ~~The problem I had~~ is ~~that I could not discover how to Zoom in and Zoom out using Screen Authoring Tools. However~~, ~~it is possible~~ to zoom ~~in using~~ JMOL commands or the Zoom command in the JMOL frank, the JMOL on the lower lefthand side of the applet. Unfortunately at this time we can only zoom in using JMOL commands in proteopedia. ( you can however, zoom in and zoom out using the commands in the console and see the results of your mastery of the command language in the applet, but when the scene is saved only the final state is saved, a bummer for now.)

If you scroll up to the original JMOL applet, and click on ADP, you will notice that the image fades allowing the ligand to become prominent as it zooms in and out while the image spins. To zoom you just need to hold down shift and then drag the molecule up and down to Zoom in the Scene Authoring Tools; <applet load='2qc8' size='300' frame='true' align='right' caption='JMOL Console Practice Applet' />. This is fine, but to have precise control of the zoom use the JMOL commands or the Zoom command in the JMOL frank, the JMOL on the lower lefthand side of the applet. Unfortunately at this time we can only zoom in using JMOL commands in proteopedia. ( you can however, zoom in and zoom out using the commands in the console and see the results of your mastery of the command language in the applet, but when the scene is saved only the final state is saved, a bummer for now.)

In the following paragraphs I will illustrate how to use several commands in JMOL which avoid some steps in the SAT. The commands i will illustrate are zoomto, select, restrict, color, translucent and... .

Revision as of 00:18, 22 December 2008 view source Tom Gluick (talk \| contribs) 404 edits →‎Assignments <ref>PDB codes for the assignment are listed in the introduction. For instance, PDB code for 1lgr may be useful in assignment 10.</ref> ← Older edit		Revision as of 00:37, 22 December 2008 view source Tom Gluick (talk \| contribs) 404 edits →‎Section 2. Using JMOL Commands in the Console Newer edit →
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	If you scroll up to the original JMOL applet, and click on ADP, you will notice that the image fades allowing the ligand to become prominent as it zooms in and out while the image spins. ~~First I dare~~ you to ~~try~~ to ~~do this using~~ the ~~Screen~~ Authoring Tools; <applet load='2qc8' size='300' frame='true' align='right' caption='JMOL Console Practice Applet' /~~> This is <scene name='User:Tom_Gluick/glutamine_synthetase/Sat_adp_transparent/1'>My attempt</scene~~>. ~~The problem I had~~ is ~~that I could not discover how to Zoom in and Zoom out using Screen Authoring Tools. However~~, ~~it is possible~~ to zoom ~~in using~~ JMOL commands or the Zoom command in the JMOL frank, the JMOL on the lower lefthand side of the applet. Unfortunately at this time we can only zoom in using JMOL commands in proteopedia. ( you can however, zoom in and zoom out using the commands in the console and see the results of your mastery of the command language in the applet, but when the scene is saved only the final state is saved, a bummer for now.)		If you scroll up to the original JMOL applet, and click on ADP, you will notice that the image fades allowing the ligand to become prominent as it zooms in and out while the image spins. To zoom you just need to hold down shift and then drag the molecule up and down to Zoom in the Scene Authoring Tools; <applet load='2qc8' size='300' frame='true' align='right' caption='JMOL Console Practice Applet' />. This is fine, but to have precise control of the zoom use the JMOL commands or the Zoom command in the JMOL frank, the JMOL on the lower lefthand side of the applet. Unfortunately at this time we can only zoom in using JMOL commands in proteopedia. ( you can however, zoom in and zoom out using the commands in the console and see the results of your mastery of the command language in the applet, but when the scene is saved only the final state is saved, a bummer for now.)

	In the following paragraphs I will illustrate how to use several commands in JMOL which avoid some steps in the SAT. The commands i will illustrate are zoomto, select, restrict, color, translucent and... .		In the following paragraphs I will illustrate how to use several commands in JMOL which avoid some steps in the SAT. The commands i will illustrate are zoomto, select, restrict, color, translucent and... .