Thanks for posting the file. I will look at it later tonight and get back to you.
Sent from my Android.
Thanks for the speedy reply. I've posted the ASCII .xyz data file,
compressed equivalent, and screen caps at
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.
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.
> -- Jason
> On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson <email@example.com> 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 18.104.22.168, 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) Jason.Vertrees@schrodinger.com
> (o) +1 (603) 374-7120