Sandbox 5 Eric Martz: Difference between revisions
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<scene name='Sandbox_5_Eric_Martz/Morph_asite_par_both_models/1'>Both empirical models</scene>. | <scene name='Sandbox_5_Eric_Martz/Morph_asite_par_both_models/1'>Both empirical models</scene>. | ||
</li><li> | </li><li> | ||
<scene name='Sandbox_5_Eric_Martz/Morph_asite_par/5'>Morph, wireframe</scene>. | <scene name='Sandbox_5_Eric_Martz/Morph_asite_par/5'>Morph, wireframe RNA</scene>. | ||
</li><li> | |||
<scene name='Sandbox_5_Eric_Martz/Morph_asite_par/6'>Morph, cartoon RNA</scene>. | |||
</li> | </li> | ||
</ul> | </ul> | ||
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The morph adds, to the two empirical models, 7 interpolated frames generated by the Yale Morph Server (see [[Morphs]]).The 9 models for the morph were uploaded as [[Image:Moran_asite_par_morph.pdb]]. Below is the script for the morph. In the [[SAT]], the uploaded PDB file was loaded, then the Jmol Console was opened, and the script below was pasted in and run (with the "load" command commented out). The morph should then animate with the desired appearance in the SAT, namely, model 1.11 (translucent PAR) should be the constant background model, and it should not be included in the animation as the last frame (without RNA). The result was then saved as a scene, leaving "animate" '''unchecked'''. (The "animate" option is using a command, 'anim on', that resets the frame range to all frames. I have requested that is use instead 'frame play' which does not.) | The morph adds, to the two empirical models, 7 interpolated frames generated by the Yale Morph Server (see [[Morphs]]).The 9 models for the morph were uploaded as [[Image:Moran_asite_par_morph.pdb]]. Below is the script for the morph. In the [[SAT]], the uploaded PDB file was loaded, then the Jmol Console was opened, and the script below was pasted in and run (with the "load" command commented out). The morph should then animate with the desired appearance in the SAT, namely, model 1.11 (translucent PAR) should be the constant background model, and it should not be included in the animation as the last frame (without RNA). The result was then saved as a scene, leaving "animate" '''unchecked'''. (The "animate" option is using a command, 'anim on', that resets the frame range to all frames. I have requested that is use instead 'frame play' which does not.) | ||
If you use the SAT to edit the representation or coloring of the morph, you will need to enter the command "frame play" in the Jmol Console just before saving the scene, leaving "animate" '''unchecked'''. | |||
The script below was developed in the Jmol ''application'' (Jmol.jar). The script will play offline if you put the PDB file, Jmol.jar, and the script in a file named 1.spt all in one directory, then double click Jmol.jar, then open the Script Console (right click on the black Jmol, then click Console on Jmol's menu), and enter (in the bottom box) "script 1.spt". | The script below was developed in the Jmol ''application'' (Jmol.jar). The script will play offline if you put the PDB file, Jmol.jar, and the script in a file named 1.spt all in one directory, then double click Jmol.jar, then open the Script Console (right click on the black Jmol, then click Console on Jmol's menu), and enter (in the bottom box) "script 1.spt". | ||