[Chimera-users] protein schematic representaton

francesco oteri francesco.oteri at gmail.com
Tue Jun 11 04:04:06 PDT 2013

Thank you Elaine,
your links work perfectly!


2013/6/10 Elaine Meng <meng at cgl.ucsf.edu>

> 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:
> -----------------------------
> 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
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco

Cordiali saluti, Dr.Oteri Francesco
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