As far as I know clustalw/x can provide you with a list of scores per
residue. You can easily feed the score into the B-value column with perl
or other command line tools. I did this a couple of years ago, not being a
scripting guru it took maybe one hour and was fun.
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 30 Jan 2007, Iain Kerr wrote:
Of course, should have tried that BUT, it appears PROTSKIN has problems
everytime it encounters a gap. It now complains about res. 296 in the same
fashion (287-295 are missing from the coordinates....)
There must be a way around this...I could split all the different parts (ie.
those separated by gaps) into different files but I expect the smaller parts
will align poorly with the sequences or I'll get a similar error again....
( P.S. sorry !, posted to COOT again by accident, have fixed my address
book..)
Charlie Bond wrote:
Iain, I've never used protskin, but can you not just mutate the offending
residue in your PDB file to get protskin to run (eg in coot or pdb-mode).
Then afterwards you can manually alter the B-factor for that residue to
what it should actually be and then run grasp etc.
Cheers,
Charlie
Iain Kerr wrote:
I tried that. My protein has a mutation at res. 141, so it said:
*Error at residue 141 :
The sequence in your PDB file does not match your BLAST query sequence.
*Here is the plain sequence alignment
<http://www.mcgnmr.ca/ProtSkin/tmp/01232-sequence_alignment> derived from
it.
I deleted res. 141 and re-ran but:
*Error at residue 142 :
The sequence in your PDB file does not match your BLAST query sequence.
*Here is the plain sequence alignment
<http://www.mcgnmr.ca/ProtSkin/tmp/01232-sequence_alignment> derived from
it.
and 142 is correctly assigned !
This looked like it was going to work !
Iain
Mark Brooks wrote:
Hi,
did you try Protskin? (http://www.mcgnmr.ca/ProtSkin/)
Its a lot less hassle than Espript, and makes Grasp input files as
well as for Pymol
Good luck,
Mark
On 31/01/07, Iain Kerr <[EMAIL PROTECTED]> wrote:
I'm trying to colour a molecular surface by sequence
conservation...(sorry,
I think I incorrectly posted this to COOTBB the other day)
I've figured out how to do it in GRASP - modify the B-factor column in
the
PDB file to represent the percentage conservation and then colour the
surface by B-factor. I know ESPRIPT will make the modified file, but I'm
having trouble generating the correct one..
I am providing ESPRIPT (expert mode, %Equivalent' scoring function) with
a
CLUSTALW alignment (Aligned sequences > Main alignment file) and a PDB
file
('Aligned sequences' > 'Supplementary pdb' file). I get the error:
'Fatal error: wrong format in PDB file.'
..and the values in the B-factor (%Equivalent) column are all either 99
or
100 which is nonsense according to the alignment.
Has anyone come across this. I don't see anything wrong with my PDB
file..
Thanks,
Iain
