Dear all,
thanks a lot for all your comments and suggestions for the alignment. I tested
already the pdb server, which works great and I am currently installing a few
other programs mentioned (Chimera, Prosmart.) for comparison.
Best Regards
Christian
Am Freitag 13 Juli 2012 16:30:57
: Re: [ccp4bb] strict structure based alignment
On Jul 13, 2012, at 4:00 PM, Christian Roth wrote:
I want align a couple or protein structures by secondary structure matching to
one target and want get a kind of aminoacid alignment file e.g. what residue
fit
the other, without adjustments due
On Jul 13, 2012, at 4:00 PM, Christian Roth wrote:
I want align a couple or protein structures by secondary structure matching
to
one target and want get a kind of aminoacid alignment file e.g. what residue
fit
the other, without adjustments due to sequence based alignments.
I tried
Dear all,
I want align a couple or protein structures by secondary structure matching to
one target and want get a kind of aminoacid alignment file e.g. what residue
fit
the other, without adjustments due to sequence based alignments.
I tried Strap, but as far as I understood it, it takes
Hi,
SSM (via PDBefold) (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver)
will do a structure based alignment and outputs a table of rmsd but will
not give you a alignment file as such.
-Sujata
On Fri, Jul 13, 2012 at 10:30 AM, Christian Roth
christian.r...@bbz.uni-leipzig.de wrote:
Dear
On 13/07/12 15:30, Christian Roth wrote:
Dear all,
I want align a couple or protein structures by secondary structure matching to
one target and want get a kind of aminoacid alignment file e.g. what residue fit
the other, without adjustments due to sequence based alignments.
I tried Strap, but
Dear Christian,
PDBefold superimposes the structures and generates the sequence
alignment in fasta(??) format. You can then read this file in Multialign
for example to get the sequence alignment and then add the secondary
structures to the sequence alignment using ESPript for example.
David
On
