[Chimera-users] Saving new coordinates after superimposing structures

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 22 17:01:24 PDT 2010

Hi Sujata,
When you save the PDB you need to save #1 "relative to" #0.  There is an option in the save PDB dialog to do this, or a similar option if you are using the "write" command to save the PDB.

To continue adding the fragments, you would just keep doing a similar procedure as described for fragments 1 and 2.  To position the third, you could just use 3x the rotation and translation that were given in the Reply Log, instead of 2x as in my example for placing the second fragment.  Or, you could instead start with the longer fragment, open two of those, and essentially do the whole thing over as described previously for the first two smaller fragments.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 22, 2010, at 4:10 PM, Sujata wrote:

> Hi,
> After I superimpose two structures using MatchMaker, I would like to save the coordinates of #1 after being superimposed with #0. When I save the PDB with the new coordinates and open #0 and #1 PDBs again, they do not superimpose.
> Can this be done? What is the best way to achieve this?
> (Elaine, I have a third fragment I want to bond to the previously bonded one and since the first-second has moved now, I want to do this so that they are on the same axis).
> Thanks,
> Sujata

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