[Chimera-users] printing "zone" search

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 13 09:17:23 PST 2007

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:

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  

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

- 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 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

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

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