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