VMD-L Mailing List

From: francesco oteri (francesco.oteri_at_gmail.com)
Date: Wed Jun 12 2013 - 09:24:32 CDT

Actually I found the good tool thank to the Chimera mailing list:

-------------------------------------
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, ...)
------------------------------------

Francesco

2013/6/12 John Stone <johns_at_ks.uiuc.edu>

>
> I don't know of a tool that would create the flattened
> 2-D figures shown in b) and d) off the top of my head,
> but one could view this is a simpler form of 2-D graph
> layout problem that there are existing software tools for.
> You're just drawing the secondary structre components as
> the "nodes" of the graph with appropriate connectivity and
> order. You could automate it to some degree by having a tool
> like STRIDE emit the secondary structure and generate a node for
> each continuous section of secondary structure.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jun 10, 2013 at 08:23:17PM +0200, francesco oteri wrote:
> > Good morning to everybody,
> > someone of you knowsA whetherA 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
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
Cordiali saluti, Dr.Oteri Francesco