sequential coloring of a range of residues
Hi, I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options: color sequential #18/P:1-10 This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P). color sequential #18:1-10/P This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10. I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number: color byattribute r:number #18/P:1-10 This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue Am I doing something wrong? Is this feature not implemented yet? Is there a work-around? Regards, Daniel N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
I can add that I only have problem with atom specifications with sequential coloring. Using the command "color #18/P:1-10 blue" works as expected and colors the designated range blue. Regards, Daniel On 2020-11-17, at 09:03, Daniel Larsson <daniel.larsson@icm.uu.se<mailto:daniel.larsson@icm.uu.se>> wrote: Hi, I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options: color sequential #18/P:1-10 This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P). color sequential #18:1-10/P This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10. I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number: color byattribute r:number #18/P:1-10 This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue Am I doing something wrong? Is this feature not implemented yet? Is there a work-around? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
It appears that Residue.number isn't registered in ChimeraX's attribute manager. That looks like a bug (will leave that to the ChimeraX team). You can work around it for now with a little tweak in the console (Tools/General/Shell): from chimerax.atomic import Residue session.attr_registration._class_builtin_types[Residue]['number']=(int,) Then your command should work - but I did run into a second bug using it when the ribbon is displayed: color_by_attr rib_colors[:, 3] = residues.ribbon_colors[:, 3] if opacity is None else opacity ValueError: could not broadcast input array from shape (852) into shape (6733) (but atoms are properly coloured) This can be worked around by repeating the command with a selection encompassing one atom per residue, e.g. color byattr r:number sel&@CA target r I'll report the issues via the bug tracker. Tristan ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Daniel Larsson <daniel.larsson@icm.uu.se> Sent: 17 November 2020 08:20 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] sequential coloring of a range of residues I can add that I only have problem with atom specifications with sequential coloring. Using the command "color #18/P:1-10 blue" works as expected and colors the designated range blue. Regards, Daniel On 2020-11-17, at 09:03, Daniel Larsson <daniel.larsson@icm.uu.se<mailto:daniel.larsson@icm.uu.se>> wrote: Hi, I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options: color sequential #18/P:1-10 This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P). color sequential #18:1-10/P This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10. I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number: color byattribute r:number #18/P:1-10 This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue Am I doing something wrong? Is this feature not implemented yet? Is there a work-around? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Daniel & Tristan, Sequential coloring of a range of residues works in recent daily builds. The changes to allow doing this with either "color sequential" (aka "rainbow") or "color byattribute" with r:number were made about a week ago. E.g. in today's daily build: open 2gbp color byattribute r:number #1/A:20-50 palette rainbow - OR - rainbow #1/A:20-50 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 17, 2020, at 12:48 AM, Tristan Croll <tic20@cam.ac.uk> wrote:
It appears that Residue.number isn't registered in ChimeraX's attribute manager. That looks like a bug (will leave that to the ChimeraX team). You can work around it for now with a little tweak in the console (Tools/General/Shell):
from chimerax.atomic import Residue session.attr_registration._class_builtin_types[Residue]['number']=(int,)
Then your command should work - but I did run into a second bug using it when the ribbon is displayed:
color_by_attr rib_colors[:, 3] = residues.ribbon_colors[:, 3] if opacity is None else opacity ValueError: could not broadcast input array from shape (852) into shape (6733)
(but atoms are properly coloured) This can be worked around by repeating the command with a selection encompassing one atom per residue, e.g.
color byattr r:number sel&@CA target r
I'll report the issues via the bug tracker.
Tristan From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Daniel Larsson <daniel.larsson@icm.uu.se> Sent: 17 November 2020 08:20 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] sequential coloring of a range of residues
I can add that I only have problem with atom specifications with sequential coloring. Using the command "color #18/P:1-10 blue" works as expected and colors the designated range blue.
Regards, Daniel
On 2020-11-17, at 09:03, Daniel Larsson <daniel.larsson@icm.uu.se> wrote:
Hi,
I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options:
color sequential #18/P:1-10
This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P).
color sequential #18:1-10/P
This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10.
I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number:
color byattribute r:number #18/P:1-10
This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue
Am I doing something wrong? Is this feature not implemented yet? Is there a work-around?
Regards, Daniel
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Ah - great! -- Tristan ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 17 November 2020 15:49 To: Tristan Croll <tic20@cam.ac.uk>; Daniel Larsson <daniel.larsson@icm.uu.se> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] sequential coloring of a range of residues Hi Daniel & Tristan, Sequential coloring of a range of residues works in recent daily builds. The changes to allow doing this with either "color sequential" (aka "rainbow") or "color byattribute" with r:number were made about a week ago. E.g. in today's daily build: open 2gbp color byattribute r:number #1/A:20-50 palette rainbow - OR - rainbow #1/A:20-50 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 17, 2020, at 12:48 AM, Tristan Croll <tic20@cam.ac.uk> wrote:
It appears that Residue.number isn't registered in ChimeraX's attribute manager. That looks like a bug (will leave that to the ChimeraX team). You can work around it for now with a little tweak in the console (Tools/General/Shell):
from chimerax.atomic import Residue session.attr_registration._class_builtin_types[Residue]['number']=(int,)
Then your command should work - but I did run into a second bug using it when the ribbon is displayed:
color_by_attr rib_colors[:, 3] = residues.ribbon_colors[:, 3] if opacity is None else opacity ValueError: could not broadcast input array from shape (852) into shape (6733)
(but atoms are properly coloured) This can be worked around by repeating the command with a selection encompassing one atom per residue, e.g.
color byattr r:number sel&@CA target r
I'll report the issues via the bug tracker.
Tristan From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Daniel Larsson <daniel.larsson@icm.uu.se> Sent: 17 November 2020 08:20 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] sequential coloring of a range of residues
I can add that I only have problem with atom specifications with sequential coloring. Using the command "color #18/P:1-10 blue" works as expected and colors the designated range blue.
Regards, Daniel
On 2020-11-17, at 09:03, Daniel Larsson <daniel.larsson@icm.uu.se> wrote:
Hi,
I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options:
color sequential #18/P:1-10
This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P).
color sequential #18:1-10/P
This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10.
I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number:
color byattribute r:number #18/P:1-10
This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue
Am I doing something wrong? Is this feature not implemented yet? Is there a work-around?
Regards, Daniel
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Many thanks! Regards, Daniel
17 nov. 2020 kl. 16:49 skrev Elaine Meng <meng@cgl.ucsf.edu>:
Hi Daniel & Tristan, Sequential coloring of a range of residues works in recent daily builds. The changes to allow doing this with either "color sequential" (aka "rainbow") or "color byattribute" with r:number were made about a week ago.
E.g. in today's daily build:
open 2gbp color byattribute r:number #1/A:20-50 palette rainbow - OR - rainbow #1/A:20-50
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 17, 2020, at 12:48 AM, Tristan Croll <tic20@cam.ac.uk> wrote:
It appears that Residue.number isn't registered in ChimeraX's attribute manager. That looks like a bug (will leave that to the ChimeraX team). You can work around it for now with a little tweak in the console (Tools/General/Shell):
from chimerax.atomic import Residue session.attr_registration._class_builtin_types[Residue]['number']=(int,)
Then your command should work - but I did run into a second bug using it when the ribbon is displayed:
color_by_attr rib_colors[:, 3] = residues.ribbon_colors[:, 3] if opacity is None else opacity ValueError: could not broadcast input array from shape (852) into shape (6733)
(but atoms are properly coloured) This can be worked around by repeating the command with a selection encompassing one atom per residue, e.g.
color byattr r:number sel&@CA target r
I'll report the issues via the bug tracker.
Tristan From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Daniel Larsson <daniel.larsson@icm.uu.se> Sent: 17 November 2020 08:20 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] sequential coloring of a range of residues
I can add that I only have problem with atom specifications with sequential coloring. Using the command "color #18/P:1-10 blue" works as expected and colors the designated range blue.
Regards, Daniel
On 2020-11-17, at 09:03, Daniel Larsson <daniel.larsson@icm.uu.se> wrote:
Hi,
I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options:
color sequential #18/P:1-10
This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P).
color sequential #18:1-10/P
This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10.
I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number:
color byattribute r:number #18/P:1-10
This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue
Am I doing something wrong? Is this feature not implemented yet? Is there a work-around?
Regards, Daniel
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Daniel Larsson -
Elaine Meng -
Tristan Croll