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
