A multiple sequence viewer incorporating structural information would be incredibly helpful, as then I wouldn't have to generate models for everything I want to compare substitutions in.
It might be too much to ask of PyMOL to be good at everything, however. Perhaps adding the ability to read in alignments from an external program (e.g. in aligned fasta format) containing the sequence of the structure (or model) to be aligned to would be sufficient? Jed Thomas Juettemann wrote: > Hi Ashok, > > there are several ways to visualise alignments. Here is a nice overview: > > Visualization of multiple alignments, phylogenies and gene family evolution > James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice > Jossinet & Geoffrey J Barton > Nature Methods 7, S16 - S25 (2010) > http://dx.doi.org/doi:10.1038/nmeth.1434 > > To address your question, it is not possible to my knowledge to upload > a sequence only to PyMOL. Keep in mind that PyMOL is a molecular > viewer, not a sequence viewer. If you want to see your sequence, you > probably would have to create a 3D model of your sequence (e.g. using > MODELLER). > > However, I think you have an interesting idea. It would be handy to > sometimes see a given sequence aligned to the structure I am looking > at. > > Question to Jason (and the community for feedback): > Would it be possible to write a module that takes one or more > sequences, aligns them to a given structure (or set) that is opened > in PyMOL and shows the aligned sequences in the sequence viewer? This > feature would be very handy for me when evaluating alignments before I > run MODELLER. > > Cheers, > Thomas > > On Tue, May 25, 2010 at 23:13, Ashok Adhikari > <ashok.adhik...@student.unsw.edu.au> wrote: > >> hi, >> >> do u know how to upload a sequence which is not in PDB. we dnt know the name >> of the sequence and we have only 250 residues ....we can align with the >> other file. we did that and we can upload those sequences from PDB but now >> we need to upload the original sequence. >> >> thanks...in advance. >> >> ashok >> from UNSW >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> 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 >> >> > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 > > -- ------------------------ Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 ------------------------------------------------------------------------------ _______________________________________________ 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
