Re: [ccp4bb]: Sequence Homology in B-factor column

[Gerard DVD Kleywegt <gerard@xray.bmc.uu.se>]

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> I wonder if there is any program/server that allows me to upload a 
> coordinates file, and then do sequence comparison with this; and output the 
> extent of homology in the B-factor column of the original PDB file.  Then I 
> can use grasp to colour it.  Please advice on this or any other method that 
> I can use to make this picture.

you can do this (and much more) with Indonesia, a Java-based workbench for
sequence and structure alignment etc. - see http://xray.bmc.uu.se/dennis/
(this particular feature was added recently so it may not be in the manual yet
- i'll ask dennis to send you a mail to explain how to do it)

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

--dvd

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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