On 12/08/2011 05:11 PM, Petr Leiman wrote:
> Dear Bostjan,
>
> There is Chimera for almost anything you can think of.
Not coot, you are sure?
Because (i) Chimera is not part of CCP4 and (ii) usually
coot does everything on this mailing list. :)
> Search for "Structure-Based Sequence Alignment" on this page:
> http://www.cgl.ucsf.edu/chimera/features.html
>
> Petr
>
>
>
> On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote:
>
>> Consurf will do this for you.
>>
>> Bostjan
>>
>> ---
>> Bostjan Kobe
>> NHMRC Research Fellow
>> Professor of Structural Biology
>> School of Chemistry and Molecular Biosciences
>>
>> and Institute for Molecular Bioscience (Division of Chemistry and
>> Structural Biology) and Centre for Infectious Disease Research
>>
>>
>> Cooper Road
>> University of Queensland
>> Brisbane, Queensland 4072
>> Australia
>> Phone: +61 7 3365 2132
>> Fax: +61 7 3365 4699
>> E-mail: [log in to unmask]
>> URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
>> Office: Building 76 Room 329
>> Notice: If you receive this e-mail by mistake, please notify me, and do
>> not make any use of its contents. I do not waive any privilege,
>> confidentiality or copyright associated with it. Unless stated otherwise,
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>>
>>
>>
>>
>>
>> On 8/12/11 3:26 PM, "Yuri Pompeu"<[log in to unmask]> wrote:
>>
>>> I once saw a figure showing the protein as surface, but instead of having
>>> it coloured by atom type
>>> or potential, it was shown by percent conservation in the family.
>>> Something like red highly conserved, all the way to white, not conserved
>>> at all...
>>> Now, I assume the figure was done by uploading aligned sequnces of
>>> several members of a family, and the colouring
>>> the generated surface accordingly.
>>> Does anyone know a way to do this more elegantly than what I tried doing?
>>> ps. I quit colouring them manually after I remebered my protein was 407
>>> aa long...
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