[Chimera-users] how to stack multiple structures into a crystal

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 29 09:40:04 PDT 2021

Hi Thiru,
If the single structure is already oriented exactly with the stack direction in Z (or X or Y) then just open multiple copies of the structure and (**without rotating the view by hand** important!!) use the "move" command to place the copies along the axis.

E.g. if the starting structure is oriented exactly so that you can stack them in Z  (in/out of screen direction), and you know they are supposed to be 35 angstroms apart, then:

open myfile.pdb
open myfile.pdb
open myfile.pdb

... then you would have models #0,1,2.  To stack (REMEMBER don't rotate the view by hand yet!):

move z 35 model #1
move z 70 model #2

If it were X or Y axis instead of Z, then you would use x or y in the command instead of z.  If you mess up you can use command "reset" and then start over with the move commands.

See "move" help:

After you are done opening/stacking, then you can rotate the view by hand.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 29, 2021, at 2:29 AM, Thirumurugan Prakasam via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hi,
> I need help to stack the crystal structures stack on top of each other. For your understanding, I have just shown the image below something like that I wanted to make. Would you please help me with how to make stacked molecular structures using chimera?
> <image.png>
> Thanks,
> Thiru

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