Hi Jason ,
Thanks for your email.
I tried this with script with around 50 pdbs - that would be around 200
objects in the final session present in 50 groups.
The proteins are all in the 14-18 kDa range and monomeric.
My async_builds is off
My auto_defer_builds is set at 500
I used two versions :
1.5.0.3 on Windows XP 64 bit
with Quadro FX 880M
And
1.4.1 on a 64 bit Ubuntu Machine
With Quadro FX 3700
On both versions and machines I had the same behavior.
The Interesting thing is that, in the final session rotation is very
smooth ..and all the object seem to be loaded and responding fine. Its only
that most of the objects dont seem to be encompassed by "all"..So hiding
everything is not possible in this session rendering the session very
cluttered and the groups un-useable. Any idea what else may be affecting
my session.
Thanks
Hari
On Thu, Mar 15, 2012 at 11:13 AM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> 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
> > Cloud computing makes use of virtualization - but cloud computing
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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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