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 <mailto: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_chime... <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chime...> >
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 <mailto: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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