Iain,
Like Dante said, you can use the ConSurf server to easily generate your
pdb with a conservation score in the b-factor column and then use the
script color_b.py (http://adelie.biochem.queensu.ca/~rlc/work/pymol/) to
make the figure with pymol.
Marcos
Iain Kerr 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
>
>
|