colour palette of multiple models
Dear Chimera-X users !
I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs.
In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot).
Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ?
Many thanks in advance
Enrico
Hello, I'm not sure why the auto-coloring makes so many shades of green. The autocoloring is in the code and somebody else would have to advise on how to change that.
A possible noncoding solution would be to use the "rainbow" command with specified palette. There are lots of palette choices, although I don't know if any will give what you want in this situation. Examples:
rainbow structures rainbow structures palette paired-12 rainbow structures palette cornflowerblue:red:gold
As shown in the third example, you can give as many colors as you want by individual color names (spaces removed) separated by colons.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2023, at 8:51 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Chimera-X users !
I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs.
In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot).
Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ?
Many thanks in advance
Enrico <Capture d’écran du 2023-07-17 17-49-29.png>
I’ve just committed a change to improve the variety of colors once you get past the builtin color list for the first 12 models. The change will be in tomorrow’s daily build. Elaine’s suggestions are still probably the best idea for your system though.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 17, 2023, at 9:51 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I'm not sure why the auto-coloring makes so many shades of green. The autocoloring is in the code and somebody else would have to advise on how to change that.
A possible noncoding solution would be to use the "rainbow" command with specified palette. There are lots of palette choices, although I don't know if any will give what you want in this situation. Examples:
rainbow structures rainbow structures palette paired-12 rainbow structures palette cornflowerblue:red:gold
As shown in the third example, you can give as many colors as you want by individual color names (spaces removed) separated by colons.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2023, at 8:51 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Chimera-X users !
I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs.
In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot).
Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ?
Many thanks in advance
Enrico <Capture d’écran du 2023-07-17 17-49-29.png>
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Great, thank you very much Elaine !
Just a quick question regarding the second example: what is the 12 in the paired-12 ?
All the best
Enrico
Il giorno lun 17 lug 2023 alle ore 19:20 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
I’ve just committed a change to improve the variety of colors once you get past the builtin color list for the first 12 models. The change will be in tomorrow’s daily build. Elaine’s suggestions are still probably the best idea for your system though.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Jul 17, 2023, at 9:51 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I'm not sure why the auto-coloring makes so many shades of green. The autocoloring is in the code and somebody else would have to advise on how to change that.
A possible noncoding solution would be to use the "rainbow" command with specified palette. There are lots of palette choices, although I don't know if any will give what you want in this situation. Examples:
rainbow structures rainbow structures palette paired-12 rainbow structures palette cornflowerblue:red:gold
As shown in the third example, you can give as many colors as you want by individual color names (spaces removed) separated by colons.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2023, at 8:51 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Chimera-X users !
I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs.
In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot).
Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ?
Many thanks in advance
Enrico <Capture d’écran du 2023-07-17 17-49-29.png>
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hello, The "palette" documentation explains this in more detail (link below) but briefly, the ColorBrewer palettes include the choice of the number of colors to spread out over the models or chains or residues depending on what you are coloring, and you could specify a different number of colors than the maximum available for that palette. 12 is the maximum available for the palette named "paired" -- there are many other palettes with different numbers of colors available. For the colors in each of the palettes specifically, see the documentation:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/palettes.html#colorbrewer
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2023, at 3:18 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
Great, thank you very much Elaine !
Just a quick question regarding the second example: what is the 12 in the paired-12 ?
All the best
Enrico
Il giorno lun 17 lug 2023 alle ore 19:20 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
I’ve just committed a change to improve the variety of colors once you get past the builtin color list for the first 12 models. The change will be in tomorrow’s daily build. Elaine’s suggestions are still probably the best idea for your system though.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Jul 17, 2023, at 9:51 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I'm not sure why the auto-coloring makes so many shades of green. The autocoloring is in the code and somebody else would have to advise on how to change that.
A possible noncoding solution would be to use the "rainbow" command with specified palette. There are lots of palette choices, although I don't know if any will give what you want in this situation. Examples:
rainbow structures rainbow structures palette paired-12 rainbow structures palette cornflowerblue:red:gold
As shown in the third example, you can give as many colors as you want by individual color names (spaces removed) separated by colons.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2023, at 8:51 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Chimera-X users !
I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs.
In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot).
Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ?
Many thanks in advance
Enrico <Capture d’écran du 2023-07-17 17-49-29.png>
Okay, thank you very much, Elaine !
Cheers,
Enrico
Il giorno mar 18 lug 2023 alle ore 17:38 Elaine Meng meng@cgl.ucsf.edu ha scritto:
Hello, The "palette" documentation explains this in more detail (link below) but briefly, the ColorBrewer palettes include the choice of the number of colors to spread out over the models or chains or residues depending on what you are coloring, and you could specify a different number of colors than the maximum available for that palette. 12 is the maximum available for the palette named "paired" -- there are many other palettes with different numbers of colors available. For the colors in each of the palettes specifically, see the documentation:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/palettes.html#colorbrewer
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2023, at 3:18 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
Great, thank you very much Elaine !
Just a quick question regarding the second example: what is the 12 in the paired-12 ?
All the best
Enrico
Il giorno lun 17 lug 2023 alle ore 19:20 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
I’ve just committed a change to improve the variety of colors once you get past the builtin color list for the first 12 models. The change will be in tomorrow’s daily build. Elaine’s suggestions are still probably the best idea for your system though.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Jul 17, 2023, at 9:51 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I'm not sure why the auto-coloring makes so many shades of green. The autocoloring is in the code and somebody else would have to advise on how to change that.
A possible noncoding solution would be to use the "rainbow" command with specified palette. There are lots of palette choices, although I don't know if any will give what you want in this situation. Examples:
rainbow structures rainbow structures palette paired-12 rainbow structures palette cornflowerblue:red:gold
As shown in the third example, you can give as many colors as you want by individual color names (spaces removed) separated by colons.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2023, at 8:51 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Chimera-X users !
I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs.
In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot).
Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ?
Many thanks in advance
Enrico <Capture d’écran du 2023-07-17 17-49-29.png>
After carefully looking on the available palettes I have an additional question: would it be possible to use other palettes not presented in the list on Chimera-X website or alternatively import them directly from the link mentioned there ?
Yours sincerely
Enrico
Il giorno mar 18 lug 2023 alle ore 17:40 Enrico Martinez jmsstarlight@gmail.com ha scritto:
Okay, thank you very much, Elaine !
Cheers,
Enrico
Il giorno mar 18 lug 2023 alle ore 17:38 Elaine Meng meng@cgl.ucsf.edu ha scritto:
Hello, The "palette" documentation explains this in more detail (link below) but briefly, the ColorBrewer palettes include the choice of the number of colors to spread out over the models or chains or residues depending on what you are coloring, and you could specify a different number of colors than the maximum available for that palette. 12 is the maximum available for the palette named "paired" -- there are many other palettes with different numbers of colors available. For the colors in each of the palettes specifically, see the documentation:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/palettes.html#colorbrewer
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2023, at 3:18 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
Great, thank you very much Elaine !
Just a quick question regarding the second example: what is the 12 in the paired-12 ?
All the best
Enrico
Il giorno lun 17 lug 2023 alle ore 19:20 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
I’ve just committed a change to improve the variety of colors once you get past the builtin color list for the first 12 models. The change will be in tomorrow’s daily build. Elaine’s suggestions are still probably the best idea for your system though.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Jul 17, 2023, at 9:51 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I'm not sure why the auto-coloring makes so many shades of green. The autocoloring is in the code and somebody else would have to advise on how to change that.
A possible noncoding solution would be to use the "rainbow" command with specified palette. There are lots of palette choices, although I don't know if any will give what you want in this situation. Examples:
rainbow structures rainbow structures palette paired-12 rainbow structures palette cornflowerblue:red:gold
As shown in the third example, you can give as many colors as you want by individual color names (spaces removed) separated by colons.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2023, at 8:51 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Chimera-X users !
I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs.
In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot).
Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ?
Many thanks in advance
Enrico <Capture d’écran du 2023-07-17 17-49-29.png>
Hi Enrico, I thought we had all of the Colorbrewer palettes. Are you seeing something there that is not in ChimeraX?
Also even if it is not built into ChimeraX by name, you can specify any palette colors you like in the command, simply by separating the multiple color specifications by colons. I gave one example earlier of built-in color names separated by colons, but the color names could instead be hex codes or rgb values or any other of these types of color specification: https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 19, 2023, at 8:52 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
After carefully looking on the available palettes I have an additional question: would it be possible to use other palettes not presented in the list on Chimera-X website or alternatively import them directly from the link mentioned there ?
Yours sincerely
Enrico
Il giorno mar 18 lug 2023 alle ore 17:40 Enrico Martinez jmsstarlight@gmail.com ha scritto:
Okay, thank you very much, Elaine !
Cheers,
Enrico
Il giorno mar 18 lug 2023 alle ore 17:38 Elaine Meng meng@cgl.ucsf.edu ha scritto:
Hello, The "palette" documentation explains this in more detail (link below) but briefly, the ColorBrewer palettes include the choice of the number of colors to spread out over the models or chains or residues depending on what you are coloring, and you could specify a different number of colors than the maximum available for that palette. 12 is the maximum available for the palette named "paired" -- there are many other palettes with different numbers of colors available. For the colors in each of the palettes specifically, see the documentation:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/palettes.html#colorbrewer
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2023, at 3:18 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
Great, thank you very much Elaine !
Just a quick question regarding the second example: what is the 12 in the paired-12 ?
All the best
Enrico
Il giorno lun 17 lug 2023 alle ore 19:20 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
I’ve just committed a change to improve the variety of colors once you get past the builtin color list for the first 12 models. The change will be in tomorrow’s daily build. Elaine’s suggestions are still probably the best idea for your system though.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Jul 17, 2023, at 9:51 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I'm not sure why the auto-coloring makes so many shades of green. The autocoloring is in the code and somebody else would have to advise on how to change that.
A possible noncoding solution would be to use the "rainbow" command with specified palette. There are lots of palette choices, although I don't know if any will give what you want in this situation. Examples:
rainbow structures rainbow structures palette paired-12 rainbow structures palette cornflowerblue:red:gold
As shown in the third example, you can give as many colors as you want by individual color names (spaces removed) separated by colons.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
> On Jul 17, 2023, at 8:51 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote: > > Dear Chimera-X users ! > > I am performing visualisation of multi domain protein loaded in the > Chimera-X as different pdbs. > > In the model panel each pdb coloured differently according to the > model ID and everythings is OK for the first 11 models, while starting > from the 12th all of them are colored in green (please see the > screen-shot). > > Would it be possible to quickly change the auto-colouring of the > multiple pdbs when I load all of them directly using chimerax > workdir/*.pdb ? > > Many thanks in advance > > Enrico > <Capture d’écran du 2023-07-17 17-49-29.png>
Right, thank you very much Elaine !
With best regards,
Enrico
Il giorno mer 19 lug 2023 alle ore 18:02 Elaine Meng meng@cgl.ucsf.edu ha scritto:
Hi Enrico, I thought we had all of the Colorbrewer palettes. Are you seeing something there that is not in ChimeraX?
Also even if it is not built into ChimeraX by name, you can specify any palette colors you like in the command, simply by separating the multiple color specifications by colons. I gave one example earlier of built-in color names separated by colons, but the color names could instead be hex codes or rgb values or any other of these types of color specification: https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 19, 2023, at 8:52 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
After carefully looking on the available palettes I have an additional question: would it be possible to use other palettes not presented in the list on Chimera-X website or alternatively import them directly from the link mentioned there ?
Yours sincerely
Enrico
Il giorno mar 18 lug 2023 alle ore 17:40 Enrico Martinez jmsstarlight@gmail.com ha scritto:
Okay, thank you very much, Elaine !
Cheers,
Enrico
Il giorno mar 18 lug 2023 alle ore 17:38 Elaine Meng meng@cgl.ucsf.edu ha scritto:
Hello, The "palette" documentation explains this in more detail (link below) but briefly, the ColorBrewer palettes include the choice of the number of colors to spread out over the models or chains or residues depending on what you are coloring, and you could specify a different number of colors than the maximum available for that palette. 12 is the maximum available for the palette named "paired" -- there are many other palettes with different numbers of colors available. For the colors in each of the palettes specifically, see the documentation:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/palettes.html#colorbrewer
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2023, at 3:18 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
Great, thank you very much Elaine !
Just a quick question regarding the second example: what is the 12 in the paired-12 ?
All the best
Enrico
Il giorno lun 17 lug 2023 alle ore 19:20 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
I’ve just committed a change to improve the variety of colors once you get past the builtin color list for the first 12 models. The change will be in tomorrow’s daily build. Elaine’s suggestions are still probably the best idea for your system though.
--Eric
Eric Pettersen UCSF Computer Graphics Lab> On Jul 17, 2023, at 9:51 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote: > > Hello, > I'm not sure why the auto-coloring makes so many shades of green. The autocoloring is in the code and somebody else would have to advise on how to change that. > > A possible noncoding solution would be to use the "rainbow" command with specified palette. There are lots of palette choices, although I don't know if any will give what you want in this situation. Examples: > > rainbow structures > rainbow structures palette paired-12 > rainbow structures palette cornflowerblue:red:gold > > As shown in the third example, you can give as many colors as you want by individual color names (spaces removed) separated by colons. > > https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential > https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Jul 17, 2023, at 8:51 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote: >> >> Dear Chimera-X users ! >> >> I am performing visualisation of multi domain protein loaded in the >> Chimera-X as different pdbs. >> >> In the model panel each pdb coloured differently according to the >> model ID and everythings is OK for the first 11 models, while starting >> from the 12th all of them are colored in green (please see the >> screen-shot). >> >> Would it be possible to quickly change the auto-colouring of the >> multiple pdbs when I load all of them directly using chimerax >> workdir/*.pdb ? >> >> Many thanks in advance >> >> Enrico >> <Capture d’écran du 2023-07-17 17-49-29.png>
participants (3)
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Elaine Meng -
Enrico Martinez -
Eric Pettersen