Ribbon scaling in a script
Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks, Lothar Dr. Lothar Esser National Institutes of Health 37 Convent Dr. Rm2122B Bethesda, MD 20892
Hi Lothar, In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling" (the set of secondary-structure-associated widths etc.). That name would be saved in your preferences. Then later you can use the "ribscale" command with that name in your scripts. Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time. Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo...> However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks,
Lothar
Hi, thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok. In the meantime I came across two more things I have a hard time figuring out: Probably quite simple but somehow escaped me so far: 1. Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done? 2. I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin. Thanks, Lothar ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 1, 2021 12:43 PM To: Esser, Lothar (NIH/NCI) [E] <esserlo@mail.nih.gov> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Ribbon scaling in a script Hi Lothar, In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling" (the set of secondary-structure-associated widths etc.). That name would be saved in your preferences. Then later you can use the "ribscale" command with that name in your scripts. Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time. Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo...> However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks,
Lothar
Hi Lothar, Yes, in Chimera there are several things that are only user-adjustable in graphical interfaces but not commands. We saw that this could be a frustration for scripting, and so an explicit goal of ChimeraX is to have commands for all of the same settings that are in the GUIs. OK, back to the questions. As far as I know, there is no user-interface way of changing either of those behaviors: (1) The halfbond color partitioning behavior (sensitivity to VDW radius) might even be a bug. Perhaps it makes some sense in the context of ball-and-stick display, but certainly not for the stick representation. (2) There is also no command for adjusting the aromatic circle thickness. Maybe others can advise on whether it is possible to do what you want by editing code, and if so, how to do it. Sorry for the issues, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 9:54 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok.
In the meantime I came across two more things I have a hard time figuring out:
Probably quite simple but somehow escaped me so far:
• Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done? • I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.
Thanks, Lothar
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 1, 2021 12:43 PM To: Esser, Lothar (NIH/NCI) [E] <esserlo@mail.nih.gov> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Ribbon scaling in a script
Hi Lothar, In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling" (the set of secondary-structure-associated widths etc.). That name would be saved in your preferences. Then later you can use the "ribscale" command with that name in your scripts. Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time. Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo...>
However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks,
Lothar
Hi, okay. The split bond color is not too bad and I don't have to have aromatic rings (although they might help). Well, did you mean to I should change the source code of chimera ? Editing it may be okay but I seem to remember that the documentation said that compiling it is not easy. I generated a nice scene (not quite finished but good) and exported it as povray scene: Parse error at line 1776: no element found Segmentation fault (core dumped) I tried WebGL and got a crash too (without any additional information). Is this a problem of my system? CentOS7 7.9.2009. Thanks, Lothar ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 1, 2021 1:57 PM To: Esser, Lothar (NIH/NCI) [E] <esserlo@mail.nih.gov> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Ribbon scaling in a script Hi Lothar, Yes, in Chimera there are several things that are only user-adjustable in graphical interfaces but not commands. We saw that this could be a frustration for scripting, and so an explicit goal of ChimeraX is to have commands for all of the same settings that are in the GUIs. OK, back to the questions. As far as I know, there is no user-interface way of changing either of those behaviors: (1) The halfbond color partitioning behavior (sensitivity to VDW radius) might even be a bug. Perhaps it makes some sense in the context of ball-and-stick display, but certainly not for the stick representation. (2) There is also no command for adjusting the aromatic circle thickness. Maybe others can advise on whether it is possible to do what you want by editing code, and if so, how to do it. Sorry for the issues, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 9:54 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok.
In the meantime I came across two more things I have a hard time figuring out:
Probably quite simple but somehow escaped me so far:
• Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done? • I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.
Thanks, Lothar
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 1, 2021 12:43 PM To: Esser, Lothar (NIH/NCI) [E] <esserlo@mail.nih.gov> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Ribbon scaling in a script
Hi Lothar, In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling" (the set of secondary-structure-associated widths etc.). That name would be saved in your preferences. Then later you can use the "ribscale" command with that name in your scripts. Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time. Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo...>
However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks,
Lothar
Hi Lothar, If I understand correctly (although it's not my department per se) it is all the associated packages that cause compiling difficulties, whereas generally if somebody can point you to a few lines of python in the Chimera code itself that need to be changed, you don't have to do any compilation. As for the other problem, no idea: we generally recommend using Help.. Report a Bug which will include your Chimera version and hardware specs, and may also allow you to attach an example session or input file and enter information on any other steps that might be needed to try to reproduce the problem. Also include your e-mail address to automatically get feedback on the report. Thanks/sorry, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 11:21 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
okay. The split bond color is not too bad and I don't have to have aromatic rings (although they might help).
Well, did you mean to I should change the source code of chimera ? Editing it may be okay but I seem to remember that the documentation said that compiling it is not easy.
I generated a nice scene (not quite finished but good) and exported it as povray scene:
Parse error at line 1776: no element found Segmentation fault (core dumped)
I tried WebGL and got a crash too (without any additional information).
Is this a problem of my system? CentOS7 7.9.2009.
Thanks, Lothar From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 1, 2021 1:57 PM To: Esser, Lothar (NIH/NCI) [E] <esserlo@mail.nih.gov> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Ribbon scaling in a script
Hi Lothar, Yes, in Chimera there are several things that are only user-adjustable in graphical interfaces but not commands. We saw that this could be a frustration for scripting, and so an explicit goal of ChimeraX is to have commands for all of the same settings that are in the GUIs.
OK, back to the questions. As far as I know, there is no user-interface way of changing either of those behaviors:
(1) The halfbond color partitioning behavior (sensitivity to VDW radius) might even be a bug. Perhaps it makes some sense in the context of ball-and-stick display, but certainly not for the stick representation.
(2) There is also no command for adjusting the aromatic circle thickness.
Maybe others can advise on whether it is possible to do what you want by editing code, and if so, how to do it.
Sorry for the issues, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 9:54 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok.
In the meantime I came across two more things I have a hard time figuring out:
Probably quite simple but somehow escaped me so far:
• Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done? • I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.
Thanks, Lothar
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 1, 2021 12:43 PM To: Esser, Lothar (NIH/NCI) [E] <esserlo@mail.nih.gov> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Ribbon scaling in a script
Hi Lothar, In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling" (the set of secondary-structure-associated widths etc.). That name would be saved in your preferences. Then later you can use the "ribscale" command with that name in your scripts. Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time. Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo...>
However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks,
Lothar
The halfbond coloring is a feature and is in the Chimera C++ code in MoleculeLensModel.cpp. It would require recompiling Chimera which is extremely difficult -- might take you a few weeks effort if you are a highly knowledgable software developer. ChimeraX always splits bonds in half for coloring. Tom
On Sep 1, 2021, at 11:40 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Lothar, If I understand correctly (although it's not my department per se) it is all the associated packages that cause compiling difficulties, whereas generally if somebody can point you to a few lines of python in the Chimera code itself that need to be changed, you don't have to do any compilation.
As for the other problem, no idea: we generally recommend using Help.. Report a Bug which will include your Chimera version and hardware specs, and may also allow you to attach an example session or input file and enter information on any other steps that might be needed to try to reproduce the problem. Also include your e-mail address to automatically get feedback on the report.
Thanks/sorry, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 11:21 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
okay. The split bond color is not too bad and I don't have to have aromatic rings (although they might help).
Well, did you mean to I should change the source code of chimera ? Editing it may be okay but I seem to remember that the documentation said that compiling it is not easy.
I generated a nice scene (not quite finished but good) and exported it as povray scene:
Parse error at line 1776: no element found Segmentation fault (core dumped)
I tried WebGL and got a crash too (without any additional information).
Is this a problem of my system? CentOS7 7.9.2009.
Thanks, Lothar From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 1, 2021 1:57 PM To: Esser, Lothar (NIH/NCI) [E] <esserlo@mail.nih.gov> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Ribbon scaling in a script
Hi Lothar, Yes, in Chimera there are several things that are only user-adjustable in graphical interfaces but not commands. We saw that this could be a frustration for scripting, and so an explicit goal of ChimeraX is to have commands for all of the same settings that are in the GUIs.
OK, back to the questions. As far as I know, there is no user-interface way of changing either of those behaviors:
(1) The halfbond color partitioning behavior (sensitivity to VDW radius) might even be a bug. Perhaps it makes some sense in the context of ball-and-stick display, but certainly not for the stick representation.
(2) There is also no command for adjusting the aromatic circle thickness.
Maybe others can advise on whether it is possible to do what you want by editing code, and if so, how to do it.
Sorry for the issues, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 9:54 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok.
In the meantime I came across two more things I have a hard time figuring out:
Probably quite simple but somehow escaped me so far:
• Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done? • I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.
Thanks, Lothar
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 1, 2021 12:43 PM To: Esser, Lothar (NIH/NCI) [E] <esserlo@mail.nih.gov> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Ribbon scaling in a script
Hi Lothar, In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling" (the set of secondary-structure-associated widths etc.). That name would be saved in your preferences. Then later you can use the "ribscale" command with that name in your scripts. Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time. Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo...>
However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks,
Lothar
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participants (3)
-
Elaine Meng -
Esser, Lothar (NIH/NCI) [E] -
Tom Goddard