[Chimera-users] Solvate Tool Trouble

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 20 14:28:37 PDT 2016

Hi Mikey,
I could not reproduce this problem.

I opened 2Q1E,  started Solvate, used box TIP3PBOX size 5 with “Remove existing ions/solvent” turned on, then added hydrogens with default settings (one is automatically prompted to add hydrogens if they are missing), and several seconds later got the structure in a box of solvent.  Then I  opened another copy of 2Q1E to see if anything had changed.  I see that Solvate does change the coordinates but only as a rigid body, i.e. although the second copy was in a different place, when I superimposed the two copies of the structure with matchmaker they looked exactly the same.

So, I guess make sure it’s not simply your viewing angle that makes it seem like something changed. 

If you are sure the dimer changed, then you should use Help… Report a Bug (which would tell us your exact version of Chimera and operating system) and attach the structure you are trying to solvate unless it’s exactly the same as PDB entry 2Q1E. 
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 20, 2016, at 11:42 AM, Mike Bergman <bergm310 at umn.edu> wrote:
> Hey there.
> I am having trouble with the solvate tool. I am using a dimeric model
> (PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model
> TIP3PBOX), it squishes the dimer together. I tried different angstrom
> box sizes - 3, 5, 10, 20. Running the simulation with them overlaid
> wouldn't give me any useful data as I'm looking for the changes in the
> dimer interface.
> Is there a way I can stop it from doing this? Should I use a different
> solvate method like Shell?
> Thanks.
> Sincerely,
> Mikey Bergman

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