Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

[Rolf S. A. <rs...@gm...>]

Hi Jason,

I've also posted a screen cap of VMD with the same file loaded 

http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png

in which the correct atom count is reported. In addition, I tried this
with my licensed copy of PyMOL on my laptop (win7), also with same
(truncated) result as Linux session. Thanks again for any help you can
provide.

Cheers //Rolf

On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote:
> Hi Jason,
> 
> Thanks for the speedy reply. I've posted the ASCII .xyz data file,
> compressed equivalent, and screen caps at
> 
> http://www.ruf.rice.edu/~rsa4046/_private/pymol/
> 
> I have had some recent problems with pymol apparently hanging on this
> machine (possibly due to an opengl + nouveau-nvidia driver issue), that
> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't
> know if my problem with atom count was related. You're right, it does
> indeed seem as if the last digit is just truncated. To test if this was
> just a display issue, I also tried loading the same data file within
> pymol (without the LIBGL statement) on a remote machine (although same
> version, OS, and libraries) via ssh X-forwarding, and derived the same
> result in terms of reported number of atoms from count_atoms, although I
> don't know if such a test is really definitive. Thanks very much for any
> insight you can provide. 
> 
> Cheers //Rolf
> 
> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote:
> > Hi Rolf,
> > 
> > That's pretty strange. Any chance you can share the file? It looks
> > like PyMOL's somehow missing the last number in the result. I've
> > easily loaded millions of atoms before and got the correct atom count.
> > 
> > Cheers,
> > 
> > -- Jason
> > 
> > On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson <rs...@gm...> wrote:
> > > I am using pymol to display the surface of inorganic crystals, and
> > > have used it successfully in the past for relatively small molecules.
> > > I am not trying to display larger surfaces (>1e6 atoms), and now
> > > notice a discrepancy between the number of atoms present in and loaded
> > > from the source file, and that reported by pymol. I have included an
> > > example using a file with 1398146 atoms. VMD loads and displays the
> > > same file and reports the correct number of atom entries. However,
> > > pymol oddly reports 139814 atoms, not 1398146. However, as far as I
> > > can tell, the atoms do *appear* in the graphical display. I've posted
> > > some screen captures at
> > >
> > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png
> > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png
> > >
> > > to illustrate this. Can anyone guess at the cause of this? I am using
> > > version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1
> > > kernel, 12012MB RAM).
> > > Many thanks //Rolf
> > >
> > > ------------------------------------------------------------------------------
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> > 
> > 
> > -- 
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrödinger, LLC
> > 
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120