As far as I know clustalw/x can provide you with a list of scores per
residue. You can easily feed the score into the B-value column with perl
or other command line tools. I did this a couple of years ago, not being a
scripting guru it took maybe one hour and was fun.
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 30 Jan 2007, Iain Kerr wrote:
> 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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