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

[Thirumurugan Prakasam]

Thanks Tom for your suggestions.
Thanks,
Thiru

On Fri, Oct 29, 2021 at 10:06 PM Tom Goddard <goddard at 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 at 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 at 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 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
>>
>>
>
> --
> 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
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