But it is very doable using grep/cut, you'll just have to use the -b flag that allows you to cut columns:
grep CA xxxx.pdb | cut -b 13-26,30-54 Cheers, Tsjerk On Mon, Mar 22, 2010 at 3:58 PM, Robert Campbell <robert.campb...@queensu.ca> wrote: > Hi Jed, > > On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone <jgoldst...@whoi.edu> wrote: > >> Of course, you could just use the .pdb file as a text file: >> >> grep CA xxxx.pdb | cut -f 2,4,7,8,9 >> >> will get you the amino acid number, the amino acid identity, and x,y,z >> coordinates for the CA. > > Often this will work, but unfortunately it is not fool proof. If there is > no chain ID, if the residue numbers are greater than 999 or if there are > alternate position characters present on the atom names, then your field > counts in your "cut" command will be off. The PDB file is very strict about > which character columns contain which information and there is no requirement > for spaces between those data columns. > > Cheers, > Rob > -- > Robert L. Campbell, Ph.D. > Senior Research Associate/Adjunct Assistant Professor > Botterell Hall Rm 644 > Department of Biochemistry, Queen's University, > Kingston, ON K7L 3N6 Canada > Tel: 613-533-6821 Fax: 613-533-2497 > <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > 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 University of Groningen The Netherlands ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
