Efficient way of showing residue conservation

From: Yuri Pompeu
Date: 8 December 2011 05:26
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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From: James Stroud
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

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From: Bostjan Kobe
Consurf will do this for you.

Bostjan

---
Bostjan Kobe

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From: Petr Leiman
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

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From: Petr Leiman
Do I feel stupid! My previous message about Chimera should have been addresses to Yuri Pompeu, but not to Bostjan Kobe.

Sincerely,

Petr

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From: Boaz Shaanan
Just to add on others' tips: Consurf is interfaced to Chimera.

          Boaz

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From: Joel Sussman

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

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From: Francois Berenger
Not coot, you are sure?

Because (i) Chimera is not part of CCP4 and (ii) usually
coot does everything on this mailing list. :)

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From: Petr Leiman
Coot is beyond competition (is there any nowadays?), but it cannot do what Yuri Pompeu asked about.

Petr

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From: Mads Gabrielsen
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

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From: xaravich ivan
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

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From: Jason Vertrees
Hi Yuri,

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

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