[chimerax-users] Unit cell orientations

[Elaine Meng]

Unit Cell is for atomic coordinates from crystal structures.  The term "unit cell" refers to X-ray crystallography.

Elaine


> On Jun 4, 2021, at 12:45 PM, Silva, Chinthaka Mahesh via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Yeah. None of the buttons including 'outlie' in 'unit cell' option works. I just use 'box' option on electron density and change back to 'surface' to get an outline. 
> 
> -chinthaka 
> 
> -----Original Message-----
> From: Elaine Meng <meng at cgl.ucsf.edu> 
> Sent: Friday, June 4, 2021 11:30 AM
> To: Silva, Chinthaka Mahesh <silva228 at llnl.gov>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Unit cell orientations
> 
> In the Unit Cell tool, you can show the outline box by clicking Outline.  If the axes defined by the data are already along X, Y, or Z, you could try command 
> 
> view orient
> 
> ... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
> 
> turn y 90
> 
> However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
> 
> <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html*initial__;Iw!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujbE6fG0Q$ > <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/turn.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujinVpDsc$ >
> 
> Elaine
> 
>> On Jun 4, 2021, at 11:10 AM, Tristan Croll <tic20 at cam.ac.uk> wrote:
>> 
>> If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
>> 
>>> On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> 
>>>> On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh <silva228 at llnl.gov> wrote:
>>>> 
>>>> Hi Elaine,
>>>> Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. 
>>>> Thanks!
>>>> -chinthaka
>>> 
>>> Hi Chinthaka,
>>> (CC to chimerax-users at cgl.ucsf.edu ... please use that address for 
>>> ChimeraX questions)
>>> 
>>> Sorry, I don't understand the question.  You can build the unit cell or a block of multiple unit cells with the Unit Cell tool:
>>> <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/
>>> tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t
>>> 439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujG3jaiew$ >
>>> 
>>> The axes of the unit cell are defined in the data... it is not something that you control.  Of course, you can rotate it after you build it.
>>> 
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry University of California, San 
>>> Francisco
>>> 
>>> 
>>> 
>>> 
>>> 
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>> 
> 
> 
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