User:Eric Martz/Sandbox 19
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<StructureSection load='' size='340' side='right' caption='' scene='99/995028/Pacupp/2'> | <StructureSection load='' size='340' side='right' caption='' scene='99/995028/Pacupp/2'> | ||
- | 1. The PDB file generated by [[PACUPP]] was uploaded to Proteopedia: [[Image:2j1n cavities fine small 3 5 20 24.pdb]]. | + | 1. The PDB file generated by [[PACUPP]] was uploaded to Proteopedia: [[Image:2j1n cavities fine small 3 5 20 24.pdb]]. (The published PDB file does not have the pseudoatoms added by PACUPP.) |
2. Within PACUPP, the initial scene was modified (using PACUPP [https://www.umass.edu/microbio/chime/pacupp/command-details.pdf Peel and Extend commands]), and then a state script was saved (''write 2j1n.spt''). | 2. Within PACUPP, the initial scene was modified (using PACUPP [https://www.umass.edu/microbio/chime/pacupp/command-details.pdf Peel and Extend commands]), and then a state script was saved (''write 2j1n.spt''). | ||
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7. The previous scene was loaded in the SAT and the Jmol commands ''select protein; cartoon off;'' were issued manually, producing <scene name='99/995028/Pacupp/2'>scene #2</scene>. Nothing was done to remove PACUPP's ''echo'' text that was at the top of scene #1. Apparently Proteopedia's SAT removed it automatically. | 7. The previous scene was loaded in the SAT and the Jmol commands ''select protein; cartoon off;'' were issued manually, producing <scene name='99/995028/Pacupp/2'>scene #2</scene>. Nothing was done to remove PACUPP's ''echo'' text that was at the top of scene #1. Apparently Proteopedia's SAT removed it automatically. | ||
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+ | An alternative scene was saved showing <scene name='99/995028/Pacupp/3'>solid protein chains, scene #3</scene>. <!--(The scene was re-loaded into the SAT and re-saved, which eliminated the text put at the top by PACUPP.)--> {{font color|red|This scene could be loaded into the SAT, whereupon the top left echo text from PACUPP was gone, but THE SAVE SCENE TAB OF THE SAT BECAME UNRESPONSIVE. ???}} | ||
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+ | The previous scenes #1-3 have pseudoatoms 3.0 Å in diameter (PACUPP cavity detail "fine"). For comparison, the [[van der Waals diameter]] of a carbon atom is 3.4 Å. The shapes of the channels are more detailed when the <scene name='99/995028/Pacupp_veryfine_small/1'>pseudoatoms are only 2.4 Angstroms in diameter</scene> (PACUPP cavity detail "very fine"). Also revealed is a '''{{font color|purple|small buried cavity}}'''. | ||
</StructureSection> | </StructureSection> |
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