Hi Hari,
I've tried your script on hundreds of objects and it seems to work
fine for me. What version of PyMOL are you using?
Do you have the async_builds setting on? If so, set to what value?
What about the auto_defer_builds settings?
I wonder if your video card is out of memory.
Cheers,
-- Jason
On Fri, Mar 9, 2012 at 5:59 PM, hari jayaram <hari...@gmail.com> wrote:
> Hi I am scripting a visualization that involves roughly thirty to fifty PDB
> files with four objects each i.e 120 to 150 objects. I have a 64 bit
> machine with 16 GB RAM and a Quadro FX 3700 card running Ubuntu Lucid.
>
> At the end of the script I get a menu with what seems like all of the
> objects suitably processed and grouped.
> After this when I click "all" and say hide..everything , a whole lot of
> objects still stay displayed . Getting the ids for some of them by right
> clicking , it seems like they are not being included on the internal GUI
> menu even when I scroll to the bottom.
> These objects are clearly created by my script but it seems like they are
> not part of "all"
> Is it that "all" is not representing all of my objects because of some limit
> to number of objects that I am handling. The interesting thing is that even
> when all the objects are loaded Pymol remains very performant.
>
> Here is my script...nothing fancy but just a loader and a grouper of PDBs
> from a directory.
>
> Any help will be greatly appreciated
> Thanks
> Hari
>
>
> import cmd
> import os
> import pymol
> import re
>
> cpi = re.compile("(\d{6})")
> pymol.finish_launching()
>
> for root,dirs,files in os.walk("/home/hari/mydownloadedPDbs/"):
> for afile in files:
> print "FILE",afile
> if "pdb" in afile:
> try:
> cmd.load(os.path.join(root,afile))
> except:
> print "Problem Loading:", afile
>
> groups = []
> for i in cmd.get_names():
> try:
> group_pool = []
>
> surfdonor = "surfdonor-%s" % i[:10]
> surfname = "surf-%s" % i[:10]
> cartoon_object = "cartoon-%s" % i[:10]
> ligands = "ligands-%s" % i[:10]
> solvent = "solvent-%s" %i[:10]
>
> # Create Object for surface and cartoon
>
> cmd.copy(surfdonor,i)
> cmd.copy(cartoon_object,i)
>
> # Create selection containing ligands and make them into their own
> object
> cmd.select(ligands+"sel","organic and " + surfdonor)
> cmd.create(ligands,"(%s)"%ligands)
> cmd.delete(ligands+"sel")
> group_pool.append(ligands)
>
> # Create selection containing solvent
> cmd.select(solvent+"sel","resn HOH and " + surfdonor)
> cmd.create(solvent,"(%s)" % solvent)
> cmd.delete(solvent+"sel")
> group_pool.append(solvent)
>
> # Extract ligand object and solvent from surface clone object
> cmd.extract(surfname,"%s and not (resn HOH or organic)" % surfdonor)
> cmd.delete(surfdonor)
> group_pool.append(surfname)
> pymol.preset.ligand_cartoon(cartoon_object)
> group_pool.append(cartoon_object)
> group_pool.append(cartoon_object + "_pol_conts")
> group_pool.append(i)
> try:
> group_name = "%s%s" % (str(i[0:3]),cpi.search(i).groups()[0])
> except AttributeError:
> group_name = "group"+ i
> print group_name
> cmd.group(group_name," ".join(group_pool))
> except :
> print "Problem with" , i
>
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
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> http://www.accelacomm.com/jaw/sfnl/114/51521223/
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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