[chimerax-users] [Chimera-users] Coloring the unit cell box

Mon Nov 21 02:38:09 PST 2022

Ok, thanks anyhow, Elaine!
I think I could get a workaround: select the box and treat it as a 
surface, then activate silhouette.
Best,
Xavier

On 18/11/22 20:31, Elaine Meng wrote:
> Hrmmm... maybe this does not solve the problem. In my experiment, it 
> didn't work well on the unit cell box.  It does work for other 
> selections like on ribbons, but there is a gap between the unit cell 
> box line and the selection highight lines, at least on my computer:
>
>
> I showed the unit cell box outline as magenta and then used command: 
>  graphics selection color magenta width 5
>
> So maybe there isn't any good way of doing it other than maybe 
> postprocessing in some image-editing program like gimp or Photoshop.
> Sorry about that,
> Elaine
>
>
>> On Nov 18, 2022, at 11:04 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>
>> (switching to chimerax-users address since this is all about 
>> ChimeraX, not Chimera)
>>
>> Sorry no, there is no linewidth setting on the unit cell outline box.
>>
>> However, you can "fake it" by selecting that model so that there are 
>> green outlines to show the selection, and then changing the 
>> selection-outline color and width:
>>
>> (1) select the outline box model, e.g. as described in the previous 
>> message by checking the selection box in the Model Panel
>>
>> (2) use "graphics selection" command to change the selection-outline 
>> color and thickness
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>>> On Nov 18, 2022, at 9:12 AM, F.Xavier Gomis-Rüth via Chimera-users 
>>> <chimera-users at cgl.ucsf.edu> wrote:
>>>
>>> Thanks a lot, Elaine, this worked indeed!
>>> Just one final point: how can I make the linewidth larger? When I 
>>> make a picture, the thin lines of the box disappear.
>>> I understand ChimeraX interpretes these lines as a surface, I can 
>>> change the colour when choosing surface in the colour blow up.
>>>
>>> On 18/11/22 17:49, Elaine Meng wrote:
>>>> Hi Xavier,
>>>> As far as I can tell, it is exactly the same in ChimeraX as in 
>>>> Chimera.  First, make sure you aren't using a very old version of 
>>>> ChimeraX.  I tried it in ChimeraX 1.5 release candidate 
>>>> (2022-11-08)  just now:
>>>>
>>>> - open your structure that has unit cell information, e.g. 1fav
>>>>
>>>> - in Unit Cell tool (menu: Tools... Higher-Order Structure... Unit 
>>>> Cell) click Outline to show unit cell box
>>>>
>>>> - if you want to change box outline color, can use the same method 
>>>> as described below for Chimera. I wasn't able to select it by 
>>>> Ctrl-click, however, so instead use the selection (hand with green 
>>>> dot) checkbox in the Model Panel to select it, then use Actions... 
>>>> Color... [...].    Or, you can just click the color square in the 
>>>> Model Panel and use the system color chooser to change the color 
>>>> interactively.   Screenshot:
>>>>
>>>> <Screen Shot 2022-11-18 at 8.48.02 AM.png>
>>>>
>>>>
>>>> I hope this helps,
>>>> Elaine
>>>> -----
>>>> Elaine C. Meng, Ph.D.
>>>> UCSF Chimera(X) team
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>>
>>>> P.S. for ChimeraX questions specifically, you may want to use the 
>>>> other mailing list, chimerax-users at cgl.ucsf.edu
>>>>
>>>>> On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users 
>>>>> <chimera-users at cgl.ucsf.edu> wrote:
>>>>>
>>>>> Dear Elaine,
>>>>> I am now trying to get this done in ChimeraX where there is indeed 
>>>>> a similar option. Unfortunately, if I proceed as in the instructions
>>>>> I do not get the cell box, in contrast with old Chimera. I also 
>>>>> tried through the command line but unsuccessfully.
>>>>> Am I missing something?
>>>>> Thanks a lot in advance,
>>>>> Xavier
>>>>>
>>>>> On 26/10/22 17:45, Elaine Meng wrote:
>>>>>> Hi Xavier,
>>>>>> You can select the box (Ctrl-click on it) and then use menu: 
>>>>>> Actions... Color... [choose color], then clear selection by 
>>>>>> Ctrl-click on blank area of window or menu Select... Clear Selection.
>>>>>> 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 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via 
>>>>>>> Chimera-users <chimera-users at cgl.ucsf.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>> Dear all,
>>>>>>> is there a way in Chimera or ChimeraX to get the unit-cell box 
>>>>>>> being drawn in another colour than white?
>>>>>>> This forces the background to be dark....
>>>>>>> Thanks a lot in advance,
>>>>>>> Xavier
>>>>>>>
>>>>>
>>>>
>>>
>>> -- 
>>> <fxgr_signanew.jpg>
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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>>
>

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