 |
 |
Coot is beyond competition (is there any nowadays?), but it cannot do what Yuri Pompeu asked about. Petr On Dec 8, 2011, at 10:10 AM, Francois Berenger wrote: > 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, >>> this e-mail represents only the views of the Sender and not the views of >>> The University of Queensland. >>> >>> >>> >>> >>> >>> 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...