One possible representation is the "sausage" produced by MOLMOL. It is
meant for NMR ensembles - the thickness of sausage is directly proportional
to local RMSD. Take a look at this image:
http://www.msg.ucsf.edu/local/programs/molmol/images/tutorial_ex3.gif
MOLMOL can be downloaded from
http://www.mol.biol.ethz.ch/groups/wuthrich_group/software
At 06:31 PM 2/22/2010, Ethan Merritt wrote:
>Hi all,
>
>I am comparing 4 very similar (<1.5A rmsd) large (750 residues) structures,
>but struggling to find a way to generate a figure that conveys where they
>are most alike and where they diverge.
>
>Simply drawing a superimposed set of backbone traces results in what looks
>like colored spaghetti. I don't think that's going to work.
>
>So I had the idea of drawing a single backbone trace, or ribbon diagram,
>and coloring by the RMSD of the four C-alphas at each residue position.
>But I can't find a program that will output this as a table of numbers
>I can use. All of the multiple structure superposition programs must
>have this information internally. After all, that's what they are minimizing.
>But do any of the programs provide an option to write it out?
>
>I can get pairwise per-residue deviations by doing SSM superposition in Coot,
>but that doesn't get me to an RMSD for all four structures jointly.
>
> Ethan
>
>
>--
>Ethan A Merritt
>Biomolecular Structure Center
>University of Washington, Seattle 98195-7742
=========================================================================
| Mensur Dlakic, PhD | Tel: (406) 994-6576 |
| Department of Microbiology | Fax: (406) 994-4926 |
| Montana State University | Lab: (406) 994-6237 |
| 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur |
| Bozeman, MT 59717-3520 | E-mail: [log in to unmask] |
=========================================================================
|