[chimerax-users] Unit cell orientations

[Silva, Chinthaka Mahesh]

I know. What I meant was, I use box from electron densities to get an outline on the unit cell of the model (pdb file). 

Thanks!
-chinthaka 

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Friday, June 4, 2021 12:53 PM
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

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/c
> ommands/view.html*initial__;Iw!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8Y
> PikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujbE6fG0Q$ > 
> <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/c
> ommands/turn.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t439
> pIGkXYR2hlS6KYA0sGeIYRZ_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-sSKftEOlx8QBt8YPikZQ8
>>> t 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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