[Chimera-users] protein schematic representaton

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 10 11:51:20 PDT 2013


On Jun 10, 2013, at 11:23 AM, francesco oteri <francesco.oteri at gmail.com> wrote:

> Good morning to everybody,
> someone of you knows whether exist a program that creates schematic representation
> of a protein like the one in plot b and d of the figure:
> http://www.nature.com/nature/journal/v427/n6972/fig_tab/nature02165_F3.html
> 
> Greetings,
> Francesco

Hi Francesco,
The short answer is that Chimera does not have this feature: generation of protein topology diagrams.

However, about a year ago I spent some time looking into the available software for exactly this problem, so I will take the liberty of sharing my conclusions here even though Chimera is not involved.  Caveats are that I could have missed something, and my findings are a year old:
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PDBsum "protein" pages show topology per domain, and these images can be downloaded.  Example:
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2gbp&template=protein.html&r=wiring&l=1&chain=A
There is also a webserver for generating PDBsum-like analyses for structures that are not already in PDB, which would presumably include the diagram generation.  Not useful for high-throughput, of course...
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html
( found via this post http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg26321.html )

I found TopDraw, which is a really a sketchpad, so you still have to do a lot yourself.
http://www.ccp4.ac.uk/html/topdraw.html

There is a server for a more recent program, pro-origami, but at least in my few tests the results were bad.
http://munk.csse.unimelb.edu.au/pro-origami/

Another program TOPS isn't quite what we want (triangles and circles, not strands and cylinders), plus the website seems to be gone now  anyway.

There is a whole additional category of programs that draw "bead necklace" diagrams, often in relationship to a membrane, also not what we want.  (for example, RbDe,  TOPO2, ...)
---------------------------
One would think there should be completely automated software to do this, but the problem of layout is actually quite difficult.  My guess is that lots of people just use general diagramming software like Illustrator or Omnigraffle.

I hope this is at least informative, if not as useful as we would like...
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco




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