STAR: Biochem

For purposes we implemented experimental patch to allow running isosurface code in parallel.

To keep backward compatibility we created new command 'pisosurface' that is functional equivalent to 'isosurface', but runs surfaces asynchroniously through ScriptEvaluator.

Click here to start patched jmol RC5

To switch to parallel isosurfaces use:

set testflag1 true

To switch to serial version use:

set testflag1 false

To compare speeds try running following the code on 1a3n.pdb file:

zap


load "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1A3N";

isoSurface surfaceA select(within(chain,*:A)) ignore (within(chain,not *:A)) VDW 100 % color TRANSLUCENT 128.0 [192,208,255] NOFILL molecular;
isoSurface surfaceB select(within(chain,*:B)) ignore (within(chain,not *:B)) VDW 100 % color TRANSLUCENT 128.0 [176,255,176] NOFILL molecular;
isoSurface surfaceC select(within(chain,*:C)) ignore (within(chain,not *:C)) VDW 100 % color TRANSLUCENT 128.0 [255,192,200] NOFILL molecular;
isoSurface surfaceD select(within(chain,*:D)) ignore (within(chain,not *:D)) VDW 100 % color TRANSLUCENT 128.0 [255,255,128] NOFILL molecular;

To compare speeds try running following version of the 2B9N.pdb file:
zap

load "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=2B9N";



isosurface surfaceD select(within(chain,*:D)) ignore (within(chain,not *:D)) VDW 80 % color TRANSLUCENT 128.0 [255,255,128] NOFILL molecular;
isosurface surfaceE select(within(chain,*:E)) ignore (within(chain,not *:E)) VDW 80 % color TRANSLUCENT 128.0 [255,192,255] NOFILL molecular;
isosurface surfaceF select(within(chain,*:F)) ignore (within(chain,not *:F)) VDW 80 % color TRANSLUCENT 128.0 [176,240,240] NOFILL molecular;
isosurface surfaceG select(within(chain,*:G)) ignore (within(chain,not *:G)) VDW 80 % color TRANSLUCENT 128.0 [255,208,112] NOFILL molecular;
isosurface surfaceH select(within(chain,*:H)) ignore (within(chain,not *:H)) VDW 80 % color TRANSLUCENT 128.0 [240,128,128] NOFILL molecular;
isosurface surfaceI select(within(chain,*:I)) ignore (within(chain,not *:I)) VDW 80 % color TRANSLUCENT 128.0 [245,222,179] NOFILL molecular;
isosurface surfaceN select(within(chain,*:N)) ignore (within(chain,not *:N)) VDW 80 % color TRANSLUCENT 128.0 [238,130,238] NOFILL molecular;
isosurface surfaceO select(within(chain,*:O)) ignore (within(chain,not *:O)) VDW 80 % color TRANSLUCENT 128.0 [0,206,209] NOFILL molecular;
isosurface surfaceP select(within(chain,*:P)) ignore (within(chain,not *:P)) VDW 80 % color TRANSLUCENT 128.0 [0,255,127] NOFILL molecular;
isosurface surfaceQ select(within(chain,*:Q)) ignore (within(chain,not *:Q)) VDW 80 % color TRANSLUCENT 128.0 [60,179,113] NOFILL molecular;
isosurface surfaceS select(within(chain,*:S)) ignore (within(chain,not *:S)) VDW 80 % color TRANSLUCENT 128.0 [189,183,107] NOFILL molecular;
isosurface surfaceT select(within(chain,*:T)) ignore (within(chain,not *:T)) VDW 80 % color TRANSLUCENT 128.0 [0,100,0] NOFILL molecular;
isosurface surfaceW select(within(chain,*:W)) ignore (within(chain,not *:W)) VDW 80 % color TRANSLUCENT 128.0 [128,0,128] NOFILL molecular;
isosurface surfaceX select(within(chain,*:X)) ignore (within(chain,not *:X)) VDW 80 % color TRANSLUCENT 128.0 [0,128,128] NOFILL molecular;
isosurface surfaceY select(within(chain,*:Y)) ignore (within(chain,not *:Y)) VDW 80 % color TRANSLUCENT 128.0 [184,134,11] NOFILL molecular;
isosurface surfaceZ select(within(chain,*:Z)) ignore (within(chain,not *:Z)) VDW 80 % color TRANSLUCENT 128.0 [178,34,34] NOFILL molecular;
isosurface surfaceR select(within(chain,*:R)) ignore (within(chain,not *:R)) VDW 80 % color TRANSLUCENT 128.0 [0,0,139] NOFILL molecular;
isosurface surfaceU select(within(chain,*:U)) ignore (within(chain,not *:U)) VDW 80 % color TRANSLUCENT 128.0 [128,0,0] NOFILL molecular;
isosurface surfaceV select(within(chain,*:V)) ignore (within(chain,not *:V)) VDW 80 % color TRANSLUCENT 128.0 [128,128,0] NOFILL molecular;
isosurface surface2 select(within(chain,*:2)) ignore (within(chain,not *:2)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface3 select(within(chain,*:3)) ignore (within(chain,not *:3)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface0 select(within(chain,*:0)) ignore (within(chain,not *:0)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface4 select(within(chain,*:4)) ignore (within(chain,not *:4)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface5 select(within(chain,*:5)) ignore (within(chain,not *:5)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface5 select(within(chain,*:5)) ignore (within(chain,not *:5)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface6 select(within(chain,*:6)) ignore (within(chain,not *:6)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface7 select(within(chain,*:7)) ignore (within(chain,not *:7)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface8 select(within(chain,*:8)) ignore (within(chain,not *:8)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surface9 select(within(chain,*:9)) ignore (within(chain,not *:9)) VDW 80 % color TRANSLUCENT 128.0 [255,255,255] NOFILL molecular;
isosurface surfaceK select(within(chain,*:K)) ignore (within(chain,not *:K)) VDW 80 % color TRANSLUCENT 128.0 [205,92,92] NOFILL molecular;

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