Re: [chimerax-users] [Chimera-users] Coloring the unit cell box
(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@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@cgl.ucsf.edu
On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@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@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
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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@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@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@cgl.ucsf.edu
On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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@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@cgl.ucsf.edu <mailto:meng@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 <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@cgl.ucsf.edu <mailto:chimera-users@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@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>
On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@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@cgl.ucsf.edu <mailto:chimera-users@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@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
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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@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@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@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@cgl.ucsf.edu
On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@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@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 >>
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--
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@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@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@cgl.ucsf.edu
On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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participants (3)
-
Elaine Meng -
F.Xavier Gomis-Rüth -
Tom Goddard