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

[Thirumurugan Prakasam]

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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