Thanks Tom for your suggestions. Thanks, Thiru On Fri, Oct 29, 2021 at 10:06 PM Tom Goddard <goddard@sonic.net> wrote:
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 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_docs_UsersGuide_midas_sym.html&d=DwMFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=I7qtfA8N7Q5sp4JqE2oPCZchG4tZN6Z7nJw71FRlb-o&s=EcVad0ZZtSpjfQ7zIJAUgEf2-0-pYw1_07oRMovpmWE&e=>
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.
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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-- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358