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 <[EMAIL PROTECTED]> 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 <[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 >>>>> >>>> >>>> >>> >> >
-- 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
