Hi Spyros, > Thank you for the links, this documentation is helpful! I am not actually > creating alignments, I just choose the "Display => Sequence" option from the > external GUI menu to get the protein sequence of my PDB structure. I was > meaning to ask - for a couple of PDB structures when PyMOL loads the > structure and the sequence is displayed, sometimes several parts of it are > missing. I attach a small image as an example (there are only 5 letters > between 226 and 271), I have checked the PDB server and the sequence page > has the full information. Is this skipping parts of sequence something > internal to PyMOL?
The sequence viewer skips over incomplete residues or missing data. That is, if a residue is missing from the sequence viewer then data are missing from the PDB file. For 3p0g, you will notice that the sequence viewer goes from residue 227 to 266. This is because there's a break in the chain in the PDB file; Lines 2326 and 2327 from 3p0g.pdb show: ATOM 1631 NZ LYS A 227 30.660 30.248 18.940 1.00101.97 N ATOM 1632 N LEU A 266 23.034 24.451 21.103 1.00132.21 N which show residue 227 being right before residue 266. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on "Lean Startup Secrets Revealed." This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev _______________________________________________ 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
