[Chimera-users] protein schematic representaton
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>
> > Good morning to everybody,
> > someone of you knows whether exist a program that creates schematic
> > of a protein like the one in plot b and d of the figure:
> > 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:
> 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...
> ( found via this post
> http://email@example.com/msg26321.html )
> I found TopDraw, which is a really a sketchpad, so you still have to do a
> lot yourself.
> There is a server for a more recent program, pro-origami, but at least in
> my few tests the results were bad.
> 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
> I hope this is at least informative, if not as useful as we would like...
> 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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