[Chimera-users] Low resolution surface model

[Elaine Meng]

On May 20, 2008, at 10:21 PM, Damien Larivière wrote:
> Dear Elaine,
> Here is what I would like to do with Chimera :
>
> From Tools/Structure analysis/sequence, it is possible to copy a  
> portion of the aminoacid sequence of a protein and then to  
> highlight in an other color this portion of sequence in a high  
> resolution surface model (Actions / surface / show).
>
> I would like to highlight a given portion of sequence but in a low  
> resolution surface model. I tried High-Order Structure / Multiscale  
> models with no success.
>
> Thanks for you help and congratulations for the work you perform.
> Damien
> ------------------------------------------
> Damien Larivière
> Fourmentin-Guilbert Scientific Foundation
> 2 Av. du Pavé Neuf, 93160 Noisy-le-Grand, France
> Phone : + 33 1 43 03 06 20
> Cell phone : +33 6 82 19 81 32
> damien.lariviere at fourmentinguilbert.org
>

Hi Damien,
You can color a low-resolution surface for certain residues, but it  
takes an additional step as compared to coloring the high-resolution  
surface.  Another difference is that it is done by distance cutoff,  
because it is no longer clear exactly which atom goes with which  
point on the surface.

(1) First create the low-resolution surface.  I can think of two  
different ways:

   (a) Multiscale Models - click "Make Models" and that will create a  
separate low-res surface for each chain.  In that dialog, if you  
select "All" chains you can then edit the resolution value for those  
surfaces.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ 
framemulti.html

   (b) command "molmap" - it makes a density map from the atomic  
coordinates, which you can then display as an isosurface.  The Volume  
Viewer tool is automatically opened to show the density; in that  
tool, you can drag a bar on the histogram to change the contour  
level.  In this case, all the atoms in the structure are used, and so  
you would get one "blob" (depending on contour level, though) rather  
than separate surfaces per chain.  Volume Viewer has many additional  
options including surface smoothing (see Features... Surface and Mesh  
options).
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ 
framevolumeviewer.html

(2) Select the residues and perform the coloring.  This can be done  
exactly the same as for the high-resolution surface, and there are  
many different ways.  To select the residues, you can use the  
Sequence tool (as you described), or the Select menu, or commands; to  
perform the coloring, you can use Actions...Color or the "color"  
command.  However, the low-res surface will not be colored yet...

(3) Use Color Zone (under Tools.... Volume Data) to color the surface  
to match the atoms you just colored.  This just uses a simple  
distance cutoff and colors parts of the surface to match the closest  
atoms.  After clicking Color, you can just drag the slider to change  
the distance cutoff.

You're welcome!  I hope this helps,
Elaine

P.S. we are working on better integration of different kinds of  
surfaces, so this procedure may change in the future
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html