that's true, residue names should be right-justified. 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
