[Chimera-users] Placing a model at 0,0,0?

Divjak Maja Maja.Divjak at petermac.org
Tue Jan 14 15:18:56 PST 2020

Thanks so much Elaine, works perfectly.

Best wishes,


-----Original Message-----
From: Divjak Maja 
Sent: Wednesday, 15 January 2020 8:40 AM
To: 'chimera-users at cgl.ucsf.edu BB' <chimera-users at cgl.ucsf.edu>
Subject: RE: [Chimera-users] Placing a model at 0,0,0?

Hi Elaine,

I'm really sorry about the multiple emails. I kept getting bounce messages to my inbox, suggesting you had not received them, so I tried different email addresses. The only time I didn't get a bounce was when I sent to your personal email. I was certainly not trying to annoy anyone. 
I will try your suggestion and see how I go.

Thank you and best wishes,


-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Wednesday, 15 January 2020 3:56 AM
To: Divjak Maja <Maja.Divjak at petermac.org>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Placing a model at 0,0,0?

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Hi Maja,
Sending the same question multiple times and/or to my individual address will not make it get answered any faster.

Here is one way.  Find out the center and then move the structure to subtract the coordinates:

open 2gbp
measure center #0

… gives (in the Reply Log):
2gbp opened
Center of mass of 2575 atoms in 2gbp (#0) coordinate system = (35.20, 30.11, 49.16)

DO NOT move the structure at all with the mouse.  Only use these commands to subtract the coordinates reported for the center:

move x -35.2
move y -30.11
move z -49.16

Then write a PDB file of the transformed coordinates, e.g. File… Save PDB, turn OFF the option “Use untransformed coordinates”.  You can also save pdb with the “write” command:

Then when you open that new structure in Chimera and measure center, it will be reported as 0,0,0. I don’t use Maya but I assume that is what you needed.

This is a rather manual approach. You could write a script to do it more automatically but that would require python rather than commands since you don’t know ahead of time what the center coordinates of each structure will be.  Somebody else would have to advise on python.  If you only have a few, might as well use this  manual approach.

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

> On Jan 13, 2020, at 11:50 PM, Divjak Maja <Maja.Divjak at petermac.org> wrote:
> Hi there,
> I’m not sure this is possible, but what I would like to do is edit molecules in Chimera, position them at 0,0,0, save the PDB and then import the molecules into Maya, so that they are positioned at 0,0,0 in the viewport, instead of in some random position away from the work grid. I can actually edit molecules, then position them by eye in the Chimera viewport and save as PDB, which will position them near the grid in roughly the right orientation when imported into Maya. So what I’m looking for is a way of setting the molecules exactly to 0,0,0 in Chimera, so that they appear at 0,0,0 when imported into Maya. I’m not sure this is actually a valid concept in Chimera?
> Thanks so much for your help and best wishes, Maja

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