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 <[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
>>>>
>>>
>>>
>>
>
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