Re: [ccp4bb] Efficient way of showing residue conservation
I input the alignment in ESPript. Add the template PDB file and it makes a Bcol.pdb file where temperature factors are replaced my sequence similarity. I open this file in Pymol in Surface and color B-Factors as rainbow. Ivan On 12/7/11, Yuri Pompeu yuri.pom...@ufl.edu 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...
Re: [ccp4bb] Efficient way of showing residue conservation
Hi Yuri, 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... PyMOL can do this pretty easily now. First you need to calculate an alignment, then you need to do the coloring. The alignment step is done like this: align protA, protB, object=aln I then wrote a script to automate the coloring of residues by conservation in the sequence alignment. You can find the script on the PyMOLWiki, here http://pymolwiki.org/index.php/Color_by_conservation. The script does a couple other useful things like showing the conservation not only by color but by cartoon putty radius, and expanding the alpha-carbon conservation to surface colors. You can find an example to copy/paste into PyMOL on that page. Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Efficient way of showing residue conservation
Dear Bostjan, There is Chimera for almost anything you can think of. 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: b.k...@uq.edu.au 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 yuri.pom...@ufl.edu 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...
Re: [ccp4bb] Efficient way of showing residue conservation
Do I feel stupid! My previous message about Chimera should have been addresses to Yuri Pompeu, but not to Bostjan Kobe. Sincerely, Petr On Dec 8, 2011, at 6:26 AM, Yuri Pompeu 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...
Re: [ccp4bb] Efficient way of showing residue conservation
Just to add on others' tips: Consurf is interfaced to Chimera. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yuri Pompeu [yuri.pom...@ufl.edu] Sent: Thursday, December 08, 2011 7:26 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Efficient way of showing residue conservation 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...
Re: [ccp4bb] Efficient way of showing residue conservation
8-Dec-2011 10:40am Dear Bostjan Consurf is also interfaced to Proteopedia, http://www.proteopedia.org, i.e. for all structures that have at least several sequences, one can automatically see an evolutionarily colored 3D Jmol image of the structures by just pushing the ConSurf button. See, e.g. http://proteopedia.org/wiki/index.php/1hho the STRUCTURE OF HUMAN OXYHAEMOGLOBIN AT 2.1 ANGSTROMS RESOLUTION by Boaz Shaanan and click on button Evolutionary conservation: [show] best regards, Joel On 8 Dec 2011, at 07:39, 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: b.k...@uq.edu.aumailto:b.k...@uq.edu.au 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 yuri.pom...@ufl.edumailto:yuri.pom...@ufl.edu 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...
Re: [ccp4bb] Efficient way of showing residue conservation
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: b.k...@uq.edu.au 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 Pompeuyuri.pom...@ufl.edu 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...
Re: [ccp4bb] Efficient way of showing residue conservation
I believe Charlie Bond's ALINE (http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) will let you make a nicely coloured sequence alignement, and then write out a Pymol script which will colour the surface by conservation. Mads -- Mads Gabrielsen, PhD Institute of Infection, Immunology and Inflammation College of Medical, Veterinary and Life Sciences University of Glasgow Room B216 /L303 GBRC 120 University place G12 8TA Phone: 0141 3307264 / 6180 E-mail: mads.gabriel...@glasgow.ac.uk On 08/12/2011 05:26, Yuri Pompeu yuri.pom...@ufl.edu 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...
Re: [ccp4bb] Efficient way of showing residue conservation-thank you everyone
On Thu, 8 Dec 2011 09:19:57 +, Mads Gabrielsen wrote: I believe Charlie Bond's ALINE (http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) will let you make a nicely coloured sequence alignement, and then write out a Pymol script which will colour the surface by conservation. Mads -- Mads Gabrielsen, PhD Institute of Infection, Immunology and Inflammation College of Medical, Veterinary and Life Sciences University of Glasgow Room B216 /L303 GBRC 120 University place G12 8TA Phone: 0141 3307264 / 6180 E-mail: mads.gabriel...@glasgow.ac.uk On 08/12/2011 05:26, Yuri Pompeu yuri.pom...@ufl.edu 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... -- Yuri Pompeu
[ccp4bb] Efficient way of showing residue conservation
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...
Re: [ccp4bb] Efficient way of showing residue conservation
Usually you put a statistic like this in the tempFactor field (B) and then color by B-factor in pymol or similar. I'm certain there is a facility for filling this entry somewhere. If not, then a fairly trivial server is waiting for someone to create it and claim the glory. Google something like alignment b-factor or clustal b-factor. That's my best guess. James On Dec 7, 2011, at 10:26 PM, Yuri Pompeu 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...
Re: [ccp4bb] Efficient way of showing residue conservation
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: b.k...@uq.edu.au 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 yuri.pom...@ufl.edu 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...
