Hi, On Wed, May 18, 2011 at 6:00 AM, Thomas Holder <spel...@users.sourceforge.net> wrote: > that's true, residue names should be right-justified.
This is a bug. Please file it on our open-source bug tracker http://sourceforge.net/tracker/?group_id=4546&atid=104546. I will fix it when I get the chance. Cheers, -- Jason > > http://www.wwpdb.org/documentation/format32/sect1.html > > "Residue name One of the standard amino acid or nucleic > acids, as listed below, or the non-standard group designation as > defined in the HET dictionary. Field is right-justified." > > Cheers, > Thomas > > On 05/17/2011 07:44 PM, Pascal Auffinger wrote: >> Hi Jason, >> >> A more difficult one (at least for me) >> Pymol seems to write (through save command) nucleic acid residue names >> not as suggested by PDB convention. >> >> Here is an extract of a PDB file (any PDB file containing nucleic acid >> residues shows the same – try 100D for example) >> >> ATOM 1 O5' C A 1 -4.549 5.095 4.262 1.00 28.71O >> ATOM 2 C5' C A 1 -4.176 6.323 3.646 1.00 27.35C >> ATOM 3 C4' C A 1 -3.853 7.410 4.672 1.00 24.41C >> >> When I save this file (save command in pymol) i get this >> >> Output from pymol >> >> XXXXX (this is added by me) >> ATOM 1 O5' C A 1 -4.549 5.095 4.262 1.00 28.71O >> ATOM 2 C5' C A 1 -4.176 6.323 3.646 1.00 27.35C >> ATOM 3 C4' C A 1 -3.853 7.410 4.672 1.00 24.41C >> >> In one instance, the "C" residue name is left justified and right >> justified in the other. >> Of course, this cannot happen for the three letter residue names. >> Any clue ? >> >> I tried the following : >> >> *pdb_truncate_residue_name* (boolean, default: off) controls whether or >> not PDB residue names are truncated to three letters only. >> >> with no effect >> >> Thanks for help >> >> Pascal > > -- > Thomas Holder > MPI for Developmental Biology > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ 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
