Hi Virasak, In Pymol you can change the element type to match your needs:
alter n. si, elem="si" Hope it helps, Tsjerk On Tue, Mar 22, 2011 at 2:44 PM, Virasak Dungsrikaew <vira...@gmail.com> wrote: > Hi Tsjerk, > > You are right. In my work, I almost working with XYZ format and all > programs that I used is work without a problem. Some programs can also > load a variant format with atomic number instead of atom name. I guest > that for atom name, these programs match the longest name and also > respect character case, like Ca/CA. > > Thank you for you help. > Virasak Dungsrikaew > > On Tue, Mar 22, 2011 at 8:35 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> 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 >> > -- 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
