From: Jan R. <jr...@im...> - 2004-07-21 16:21:38
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I want to compare matching surfaces and as a sandbox I used the three MODEL DNA binding protein structure 1lcd http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1lcd the script was: frame 1; select dna and */1;define prev selected;select within(group,within(8.4, prev)) and protein and */1;set solvent on;dots on; select not within(5.4, prev) and */1;dots off;select prev;cartoon 1; # this is the DNA interacting protein surface frame 2; select protein and */2;define prev selected;select within(group,within(8.4, prev)) and nucleic and */2;set solvent on;dots on; select not within(5.4, prev) and */2;dots off;select prev;cartoon 1; # this is the DNA surface in contact with the protein frame 3; restrict not */3; # I don't need this frame anim mode loop;anim fps 2;anim on; but not as expected, the dots surface persist while the rest of the rendering changes with frame. Regards, Jan |
From: Miguel <mi...@jm...> - 2004-07-21 16:48:59
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Jan wrote: > I want to compare matching surfaces and as a sandbox I used the three > MODEL DNA binding protein structure 1lcd [snip] > but not as expected, the dots surface persist while the rest of the > rendering changes with frame. That sounds like a bug. The dots rendering code is not respecting the currently displayed model. Miguel |
From: Miguel <mi...@jm...> - 2004-07-22 17:34:15
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> Jan wrote: > >> I want to compare matching surfaces and as a sandbox I used the three >> MODEL DNA binding protein structure 1lcd > [snip] > >> but not as expected, the dots surface persist while the rest of the >> rendering changes with frame. > > That sounds like a bug. The dots rendering code is not respecting the > currently displayed model. The dot surface code now works properly with multiple models(frames) in Jmol 10pre11n. Previously this code was not differentiating between atoms in different models(frames). This bug also affected the within({distance}, {set}) atom expression operator. Performance tech note --------------------- While working on this I observed some performance problems when working with macromolecules. Jan specifically asked about 1LCD. This has 3 models, each of which includes 1100 atoms (not particularly large). on a 2.8 Ghz Pentium ... load samples/pdb/1LCD.pdb select * set solvent off; dots on # VDW surface takes 1.2 seconds dots off set solvent on; dots on # Solvent Accessible Surface takes 12.2 seconds In addition, the time to render a single frame to the screen was about doubled when the SAS was displayed. This is because the current code is doing AxisAngle calculations during the rendering process to paint the saddle shapes formed between two adjacent spheres. I have no plans to work on this performance issue until we address true surfaces ... after the official v10 release. Miguel calculating the VDW surface (solvent off) takes 1.1 seconds calculate |