[Chimera-users] Untranslating after using solvate

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 29 10:57:29 PDT 2012

Hi Matt,
I believe the change in coordinates is done by Ambertools and not Chimera itself, so we don't have control over that.  However, you could open another copy of the original structure, match the solvated structure onto the original structure, and save PDB of the solvated structure "relative to" the unmodified model.

Matching could be done with MatchMaker (or mmaker command), or with the match command.  For example, if I solvated model #0, I could open another copy of that structure as model #1, then use the mmaker command to superimpose #0 onto #1:  mm #1 #0

The match should be exact (RMSD 0) since the structure is the same, ignoring solvent. Then you can save as PDB model #0 relative to model #1.


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 Jun 29, 2012, at 8:26 AM, Matthew Baumgartner wrote:

> Hello,
> I am using chimera to add a shell of water around a given protein using the solvate command through the command line. However, upon adding solvent, the protein is translated/rotated a bit, as mentioned in the documentation ( file:///opt/UCSF/Chimera64-1.6/share/chimera/helpdir/ContributedSoftware/solvate/solvate.html). However, I would like to leave the protein in it's input coordinates and simply add waters around it. 
> Is there a way to use the solvate command without translation? If not, how should I go about resetting the structure back to it's original coordinates?
> Thanks, 
> Matt

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