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
>>
>
>
