Dear Warren Thank you for your information. It works fine.
Joonghyun -----Original Message----- From: DeLano Scientific [mailto:del...@delsci.info] Sent: Sunday, October 26, 2008 3:25 AM To: 'Joonghyun Ryu'; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] question about checking the performance of PyMOL Joonghyun, To optimize performance and responsiveness, PyMOL tends to defer compute-intensive tasks until their results are actually needed. Thus, cmd.show("surface") Doesn't actually show a surface, it only sets the surface visibility flag on the atoms present (for future reference). An actual surface won't be computed until PyMOL is asked to refresh or render the display. When running a script, you can force an update by calling: cmd.refresh() After cmd.show. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -----Original Message----- From: Joonghyun Ryu [mailto:jh...@voronoi.hanyang.ac.kr] Sent: Friday, October 24, 2008 10:39 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] question about checking the performance of PyMOL Hi, all I am sending this email for asking you about checking the performance of PyMOL. I tried to check the elapsed time for the computation of a molecular surface as follows. -- import os import cmd import pymol cmd.set("surface_quality", "2") start = time.time() cmd.show("surface") end = time.time() elapsedTime = (end - start) print "Elapsed time: ", elapsedTime, "sec." -- The result always shows 0 sec. for any sized PDB file. For example, it takes about 10 sec. for 1L7A.pdb (by my watch) which contains about 5000 atoms. However, if I run the above codes in PyMOL command-line mode, it shows Elapsed time: 0 sec. Currently, I am using PyMOL 1.1b4edu (May 2008) on Windows XP. Should I use other APIs for checking the performance? ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
