[chimerax-users] Unit cell orientations

Fri Jun 4 13:32:45 PDT 2021

Okay. That helps. 

Thanks!
-chinthaka 

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Friday, June 4, 2021 1:27 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

As mentioned in the Unit Cell help (shown by clicking its Help button, or see the link I sent earlier), the tool uses SMTRY, CRYST, and/or MTRIX lines in the input PDB file, or the equivalent information read from an input mmCIF file.  If your input does not have this information, then the tool does not have any information to draw a box.

In the Volume Viewer tool with the histogram of density values, you don't need to change the style to show the box.  Just use the context menu of that tool (right-click or Ctrl-click on the histogram, depending on what kind of computer you are using) and choose "Show Outline Box."

You can try the same commands I suggested earlier (view and turn) to see if they give the orientations that you want.  If not, you would have to rotate it manually.

Elaine 

> On Jun 4, 2021, at 12:55 PM, Silva, Chinthaka Mahesh via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> I calculate electron densities using charge flipping using XRD patterns. Sorry, I was not clear before. 
> 
> -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-sSKftEOlx8QBt8
>> Y PikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujbE6fG0Q$ > 
>> <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/
>> c
>> ommands/turn.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t43
>> 9 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/use
>>>> r
>>>> /
>>>> tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ
>>>> 8 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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