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<rsa4...@gmail.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 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.vertr...@schrodinger.com
>>> (o) +1 (603) 374-7120
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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