[ccp4bb]: SUMMARY: Sequence homology in B-factor column

[Yu Wai Chen <ywc@mrc-lmb.cam.ac.uk>]

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Dear all,

The original question was how to do sequence comparison with a PDB file and 
output the residue homologies in the B-factors column in the PDB file. 
Thanks for all your responses.  Here I summarize all the answers I get.

A. Bostjan Kobe & Douglas Theobald:
   Use "ConSurf" (http://consurf.tau.ac.il/)

B. Daniel John Rigden & Alex Pautsch:
   Use "ESPript" (http://prodes.toulouse.inra.fr/ESPript/)

C. Dennis Madsen & Gerard Kleywegt:
   Use "Indonesia" (http://xray.bmc.uu.se/~dennis/)

After having installed indonesia:
1) Create a sequence alignment with the protein structure as the _first_
sequence
(you can load PDB files directly as a "sequence type" - it will extract the
sequence
from the SEQRES or ATOM cards depending on what is available).
2) Save the sequence alignment in "ODAT format" - choose "save as" in
alignment editor window and
give the file the suffix "odat" and type "ODAT".
3) Save the perl script that I have attached to this mail and do "chmod a+x
bfactor.pl"
4) Use the perl script to insert the diversity at the b-factor's place:
 ./bfactor.pl -pdb mypdbfile.pdb -odat myodatfile.odat > newpdbfile.pdb
The file "newpdbfile.pdb" will have the information you want.

D. Also from Gerard Kleywegt:
   if you have the sequence alignment already, you can also use the low-tech
approach of SOD (http://xray.bmc.uu.se/usf/sod_man.html - use task MULT) -
this will give you several O datablocks etc. to colour your CA trace by 
level
of sequence conservation or variability

E. Rob Meijers:
   a quick'n dirty way, when you have a pdb file and an alignment in
clustalx aln format, is to go to:
http://www.mifoundation.org/Tools/index_frames
choose the option: h2pdb, upload your files, and you'll get either an email 
or a downloadable PDB file with the B factor modified according to 
variability, based on
Shannon's entropy.

F. Titia:
   I think with Whatif you can get a MAXHOM score (use the PHD/predict 
protein server to get this) in the B-factor column. If it is not an 
official option ask Gert Vriend about it, they have made it in the past. 
We used to do it with a one line awk script ourselves (Tong et al, JBC, 
1997, 272, 21381-21387.)



===================================================================
Yu Wai CHEN, Ph.D. ..................   email:ywc@mrc-lmb.cam.ac.uk
 Centre for Protein Engineering,             tel:+44-(0)1223-402148
 MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140
 WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc