Hi Kelvin, the "psico" module provides a "fasta" command which maintains the gaps. However, psico will not work with PyMOL 0.99 which is quite old and uses an ancient Python version (psico requires Python 2.6 and and the PyMOL 1.2 API).
Psico installations instructions and download link: http://pymolwiki.org/index.php/Psico Cheers, Thomas On 31 Mar 2014, at 05:13, Kelvin Luther <klut...@access.uzh.ch> wrote: > Hello, > > I am using PyMOL 0.99rc6. I am wondering if there is a means to obtain > a FASTA sequence from a loaded pdb file that maintains the gaps due to > missing portions of the structure? I found one program that will strip > the sequence from pdb files, but it simply reads out the amino acids > that are present linearly. Gaps in the sequence are not maintained. I > can't imagine why that would be useful. I have a large number of pdb > files to deal with and would like to avoid having to align each pdb > sequence to the gene just to recover the gaps. > > Thanks for your time, > > -- > Kelvin Luther > Physiologische Institut > Universität Zürich -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ _______________________________________________ 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
