Hi,
pymol.cmd.refresh() doesn't work when the function is placed before
cmd.png(), but works when placed after.
As cmd.refresh() is much faster than time.sleep(1), the script is now
quicker (I used this function to get the 2D pictures from a sdf file
containing less than 100 structures).
here is now the corrected script :
def mol2png(ctfile,name):
pymol.cmd.read_molstr(ctfile,name)
pymol.cmd.set("valence",1)
pymol.cmd.hide("all")
pymol.cmd.show("sticks")
pymol.cmd.set("stick_radius",1)
pymol.cmd.color("black","elem c")
pymol.cmd.color("red","elem o")
pymol.cmd.color("blue","elem n")
pymol.cmd.color("yellow","elem s")
pymol.cmd.bg_color("white")
pymol.cmd.zoom(name)
pymol.cmd.ray()
pymol.cmd.png(name)
pymol.cmd.refresh()
pymol.cmd.delete(name)
Works fine with a Centrino (1.6GHz) laptop and Linux Debian (sarge).
Thanks,
Jerome Pansanel
Selon Warren DeLano <war...@delsci.com>:
> Jerome,
>
> Try calling
>
> pymol.cmd.refresh()
>
> before
>
> pymol.cmd.png(name)
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
>
>
> > -----Original Message-----
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > Jerome PANSANEL
> > Sent: Friday, January 06, 2006 5:06 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] Python scripting for Pymol
> >
> > Hi,
> >
> > I writing a small script in python, in order to export png
> > picture from a MDL sdfile.
> > Here is a sample of the function :
> >
> > def mol2png(ctfile,name):
> > pymol.cmd.read_molstr(ctfile,name)
> > pymol.cmd.set("valence",1)
> > pymol.cmd.color("black","elem c")
> > pymol.cmd.color("red","elem o")
> > pymol.cmd.color("blue","elem n")
> > pymol.cmd.color("yellow","elem s")
> > pymol.cmd.bg_color("white")
> > pymol.cmd.zoom(name)
> > pymol.cmd.png(name)
> > time.sleep( 1 )
> > pymol.cmd.delete(name)
> >
> >
> > It works fine only if I have the function time.sleep(1). If
> > not, I have only empty pictures. Is there another solution to
> > delete the molecule only when the png file has been written ?
> >
> > Thanks,
> >
> > Jerome Pansanel
> >
> >
> >
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>
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