Hi Thomas,
Your patch got the file loaded in its entirety, thanks!
$ pymol $SIM -c -d "@./png.pml"
ExecutiveLoad: "output/flicker-1811000.xyz" loaded as "flicker-1811000", through state 1.
PyMOL>@./png.pml
Selector: selection "cube" defined with 1398146 atoms.
PyMOL>count_atoms cube
Selector: selection "cube" defined with 1398146 atoms.
count_atoms: 1398146 atoms
...
I posted the result at
http://www.ruf.rice.edu/~rsa4046/_private/pymol/flicker-1811000.png
Thanks again-
Cheers //Rolf
On Thu, Apr 19, 2012 at 12:11:56PM -0500, Rolf S. Arvidson wrote:
> Hi Thomas,
> Thanks very much for this patch, I will apply and post back results. Cheers!
> // Rolf
>
> On Thu, Apr 19, 2012 at 11:46 AM, Thomas Holder
> <speleo3@...> wrote:
> > Hi Rolf,
> >
> > the count_atoms command is fine. PyMOL truncates the first line of the
> > xyz file to 6 characters, so it actually stopped reading the file after
> > 139814 atoms. The fix is easy:
> >
> > --- layer2/ObjectMolecule.c (revision 3996)
> > +++ layer2/ObjectMolecule.c (working copy)
> > @@ -3481,7 +3481,7 @@
> > atInfo = *atInfoPtr;
> >
> > p_store = p;
> > - p = ncopy(cc, p, 6);
> > + p = ncopy(cc, p, 9);
> > if(sscanf(cc, "%d", &nAtom) != 1) {
> > nAtom = 0;
> > tinker_xyz = false;
> >
> > Cheers,
> > Thomas
> >
> > On 04/19/2012 04:00 PM, Rolf S. Arvidson wrote:
> >> 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<rsa4046@...> 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
> >>>>
> >>>> --
> >>>> Jason Vertrees, PhD
> >>>> PyMOL Product Manager
> >>>> Schrödinger, LLC
> >>>>
> >>>> (e) Jason.Vertrees@...
> >>>> (o) +1 (603) 374-7120
> >
> >
> > --
> > Thomas Holder
> > MPI for Developmental Biology
> > Spemannstr. 35
> > D-72076 Tübingen
> >
> > ------------------------------------------------------------------------------
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