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
<spel...@users.sourceforge.net> 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<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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