Re: [PyMOL] question about checking the performance of PyMOL

Dear Warren

Thank you for your information.
It works fine.

Joonghyun
-----Original Message-----
From: DeLano Scientific [mailto:de...@de...] 
Sent: Sunday, October 26, 2008 3:25 AM
To: 'Joonghyun Ryu'; pym...@li...
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:su...@de...


-----Original Message-----
From: Joonghyun Ryu [mailto:jh...@vo...] 
Sent: Friday, October 24, 2008 10:39 PM
To: pym...@li...
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?



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