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
