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

Mon Nov 21 02:38:38 PST 2022

Wow, great!
Thanks a lot, Tom!

On 18/11/22 21:03, Tom Goddard wrote:
> Hi Xavier,
>
>   The way to make thicker unit cell lines in ChimeraX is to show them 
> as cylinders using a "marker model".  If model #3 is the thin line 
> outline then this command will make the outline with cylinders
>
> marker fromMesh #3 edgeRadius 0.5 color lightyellow
>
> Documentation
>
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html
>
>   Tom
>
>
>
>> On Nov 18, 2022, at 11:31 AM, Elaine Meng via ChimeraX-users 
>> <chimerax-users at cgl.ucsf.edu> 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:
>>
>> <Screen Shot 2022-11-18 at 11.25.32 AM.png>
>>
>> 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>
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>>
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