Hi Virasak, It goes a bit far to call it a bug. It's a problem with the xyz format. It only has names for atoms, not element types, and Pymol can't go guessing, otherwise any CA would end up as calcium :S
Cheers, Tsjerk On Tue, Mar 22, 2011 at 2:30 PM, Virasak Dungsrikaew <vira...@gmail.com> wrote: > Hi Tsjerk, > > Thank you for your quick reply. I just follow your suggestion to show > all label, apparently that it's problem in loading XYZ file format > (got S instead of Si). If I use the same structure in PDB format, it > works fine. For now, I will use only PDB in my work. > > Anyway, the XYZ file should work, because it's come from conversion of > 'babel' program with the same input as the PDB file and it seem > correct in my eyes. Is it a bug in loading XYZ file format? > > Cheers, > Virasak Dungsrikaew > > > On Tue, Mar 22, 2011 at 6:36 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> Hey Virasak, >> >> If you load the structure and do: >> >> label all, elem >> >> does the silicium show op as 'Si'? >> >> If it doesn't, you should check the input file. >> >> I did a quick test, reading in a PDB file with an atom modified to >> silicium and then saving it, which gave no problems with pymol 1.3. If >> you don't manage to solve the problem, can you isolate the silicium >> containing part, and post it together with the set of commands you >> used? >> >> Cheers, >> >> Tsjerk >> >> On Tue, Mar 22, 2011 at 11:26 AM, Virasak Dungsrikaew <vira...@gmail.com> >> wrote: >>> Dear all, >>> >>> I am using PyMOL 1.2r2 on Ubuntu 10.10. >>> When I click 'Save Molecule...' from 'File' menu and select a molecule >>> that contained 'Si' atom, the output pdb will show 'S' instead of 'Si' >>> on the right most column. >>> I also try this with mol format, the result is the same. >>> Is this a known bug or only ubuntu version bug? >>> If this is a bug, how to fixed it? >>> >>> Thanks in advance. >>> >>> Regards, >>> Virasak Dugnsrikaew >>> >>> ------------------------------------------------------------------------------ >>> Enable your software for Intel(R) Active Management Technology to meet the >>> growing manageability and security demands of your customers. Businesses >>> are taking advantage of Intel(R) vPro (TM) technology - will your software >>> be a part of the solution? Download the Intel(R) Manageability Checker >>> today! http://p.sf.net/sfu/intel-dev2devmar >>> _______________________________________________ >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>> >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
