[Chimera-users] Reading Frame Problem

[Elaine Meng]

Dear Mark,
The structures should automatically be in the same coordinate system 
(i.e. all the transformations applied by rotating and scaling 
interactively will apply to all open models, or if you haven't 
manipulated anything, they will both be in shown in their untransformed 
coordinates).

The only thing I can think of is that during preparation for GOLD 
docking, some transformation was applied to the system, resulting in 
its differing from the original coordinates of the system. You could 
try comparing the original receptor coordinates with the receptor in 
its prepared state to check for that.

If you don't think anything like that happened, it would be great if 
you could supply two example files and tell us why/how you can tell 
that they are not in a consistent coordinate system when displayed in 
Chimera.  You could send the info just to me (and I'd share it only 
with the Chimera development team) if you'd like.

When/if the structures are in the same frame of reference, you would 
then use the command "rmsd" to calculate the RMSD without performing 
fitting.
Manual page for rmsd:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html

Best,
Elaine

On Jun 9, 2006, at 4:26 PM, markcunningham wrote:

> Could someone please help with this. .
>
>   Using Chimera, I am trying to calculate rmsd between an observed
> ligand versus GOLD docked ligand, however the problem is the ligands
> load into different reading frames. The format for both ligands is
> .mol2. How can I correct this problem, in other words load both
> ligands into the same reading frame so that I can then calculate their
> rmsd.
>
> Thanks.
> Mark
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-----
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