[Chimera-users] printing "zone" search

[Elaine Meng]

Hi Francesco,
You can write out a list of what is selected with "Actions... Write  
List" or the coordinates of the selected atoms as a PDB file with  
"Actions... Write PDB".  The dialog for writing a list lets you  
choose whether you want atoms or just residues listed, and the style  
to use, as explained here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#writespec

There are several features (and corresponding parts of the  
documentation) that relate to RMSD.  If you choose "Help... Search  
Documentation" from the menu and search for "rmsd" you get a list.

 From your description, you probably want to use the command "rmsd" -  
it calculates RMSD between two sets of atoms without moving/fitting  
them.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html

Other things that relate to RMSD (see documentation if you need more  
details):

- the "match" command, which fits the two specified sets of atoms and  
then reports the resulting RMSD
- "matchmaker" command or MatchMaker tool, superimposes proteins and  
reports alpha-carbon RMSD for the residue pairs used in the fit
- EnsembleMatch tool, which calculates all pairwise RMSD values for  
specified atoms within an ensemble of structures that contain  
identical atoms
- MD Movie tool, which can calculate all pairwise RMSD values for  
selected atoms within frames of a trajectory

I hope this helps,
Elaine
-----
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

On Dec 13, 2007, at 7:49 AM, Francesco Pietra wrote:

> I am looking at the protein residues "responsible" for docking a  
> single-residue
> ligand.
>
> select protein & :ligandname z<#
>
> works for various values of #. I would like to print the list of  
> residues
> instead of having to detect them from the screen, which may lead to  
> errors.
>
> Also, which section of the manual concerns RMSD? (I would like to  
> calculate
> RMSD at various stages of DOCK6.1 and Amber9 MD for the above,  
> i..e. how the
> ligand adapts and the protein follows it, or vice-versa).
>
> Thanks
> francesco pietra