Another way to make the copies is to use the Chimera sym command.  For example,

 sym #0 group shift,5,14 axis z

copies model #0 five times at 14 Angstrom spacing along the z axis of the model #0 coordinate system (not the view direction coordinate system).

   https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html

Tom

On Oct 29, 2021, at 10:16 AM, Thirumurugan Prakasam via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Thank you so much Elaine for your quick response and help.

Many Thanks,

Thiru

On Fri, Oct 29, 2021 at 8:40 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

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:
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_move.html&d=DwIFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=W_iTL8zm-aasz2PWuQlh91HFZlluzIuOYNUkSse6VCg&s=hPTcvB8jZ7V052xezzJt_VpKl3mWKQVui_IsjGjRA_g&e= >

After you are done opening/stacking, then you can rotate the view by hand.
I hope this helps,
Elaine
-----
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@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

-- 

Thirumurugan Prakasam,
Research Scientist,
New York University Abu Dhabi,
Experimental Research Building
Building C1, Saadiyat Island
Abu Dhabi, UAE

Phone no: +971-561976358

 

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