A python script to do just that is below.
Cheers,
Stephen
== Start of script ==
#!/usr/bin/python
import os
import string
import sys
if len(sys.argv) != 3:
print 'Set the B factor column to reflect sequence conservation from CLUSTALX'
print 'Usage: colour_sequence <PDB file protein> <Q scores file>'
sys.exit(1)
PDB_file = open( sys.argv[1], "r" )
q_scores = open( sys.argv[2], "r" )
# Read all of the scores
lines = q_scores.readlines()
bfactors = []
for ln in lines:
bfactors.append( ln.split()[1] )
# Go through the PDB file and update the B Factors
for atom in PDB_file.readlines():
if atom[0:4] == "ATOM":
resid = int(atom[22:26])
new_atom = atom[:60]+"%3s.00"%(bfactors[resid-1])+atom[66:]
print new_atom,
else:
print atom,
== End of script ==
On 1/31/07, Tim Gruene <[log in to unmask]> wrote:
> 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 <[log in to unmask]> 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
> >>>>>
> >>>>
> >>>>
> >>>
> >>
> >
>
--
Dr Stephen Graham
Nuffield Medical Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549
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