display pseudobonds between atoms as solid line
Hi, I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model. I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands. I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0 but the distance does not appear on my screen. Could you help me work this out? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
Hi Vincent, The "pbond" command is only in version 1.8 or newer, according to the Change Log. Maybe what you have is too old, so get a newer ChimeraX. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> What you said should work if those atoms actually exist and the model is not hidden. Similar commands work just fine for me, e.g. open 2gbp pbond #1/A:13@O #1/A:153@O reveal true color magenta dashes 1 cartoon suppress false ("cartoon suppress false" allows showing backbone atoms at same time as cartoon) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 10, 2024, at 6:38 AM, Vincent CHAPTAL via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model.
I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands.
I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0
but the distance does not appear on my screen.
Could you help me work this out? Thank you Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
_______________________________________________ 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/
Thanks Elaine, Indeed I'm under version 1.7. Time to update! Vincent On December 10, 2024 5:57:33 PM GMT+01:00, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Vincent, The "pbond" command is only in version 1.8 or newer, according to the Change Log. Maybe what you have is too old, so get a newer ChimeraX. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>
What you said should work if those atoms actually exist and the model is not hidden. Similar commands work just fine for me, e.g.
open 2gbp pbond #1/A:13@O #1/A:153@O reveal true color magenta dashes 1 cartoon suppress false
("cartoon suppress false" allows showing backbone atoms at same time as cartoon)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 10, 2024, at 6:38 AM, Vincent CHAPTAL via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model.
I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands.
I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0
but the distance does not appear on my screen.
Could you help me work this out? Thank you Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
_______________________________________________ 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/
Hi Elaine, as a follow-up question, is it possible to show one pbond with 0 dashes, and the other one with 10 dashes. It seems like the latest command overrides the first one (also in terms of radius value): pbond #1.34:940@O #1.34:472@O reveal true color red dashes 0 radius 0.7 pbond #1.34:368@O #1.34:1044@O reveal true color red dashes 10 radius 0.5 I haven't tried yet to call these 2 pbonds from 2 different models to see if I can trick this representation. Generally, it would be useful to be able to show different kinds of argument per model, the figures are getting more complex now I feel. I'm managing to reach this by loading several time the same model and only showing the parts I'm interesting in but the script gets very messy and long, while if we can only load 1 model and modify it the way we want it would make it easier and cleaner. Thanks Vincent Le 10/12/2024 à 17:57, Elaine Meng a écrit :
Hi Vincent, The "pbond" command is only in version 1.8 or newer, according to the Change Log. Maybe what you have is too old, so get a newer ChimeraX. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>
What you said should work if those atoms actually exist and the model is not hidden. Similar commands work just fine for me, e.g.
open 2gbp pbond #1/A:13@O #1/A:153@O reveal true color magenta dashes 1 cartoon suppress false
("cartoon suppress false" allows showing backbone atoms at same time as cartoon)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 10, 2024, at 6:38 AM, Vincent CHAPTAL via ChimeraX-users<chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model.
I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands.
I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0
but the distance does not appear on my screen.
Could you help me work this out? Thank you Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
Hi Vincent, The number of dashes is the same for all pseudobonds in the same model, sorry. Hi Vincent, If you use the "name" option of the pbond command it will create a new pseudobond model with that name. So just give each one a name and it can have an independent number of dashes. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/pbond.html> Example: open 2gbp pbond #1/A:13@O #1/A:153@O reveal true color magenta dashes 0 name blah1 pbond :bgc@o1 :bgc@o4 reveal true color cyan dashes 5 name blah2 If you don't use "name" they all go into the same model named "custom" (default name), and all of the pseudobonds in the same model have the same number of dashes as each other. I hope this helps, Elaine
On Dec 11, 2024, at 4:05 AM, Vincent CHAPTAL via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
as a follow-up question, is it possible to show one pbond with 0 dashes, and the other one with 10 dashes. It seems like the latest command overrides the first one (also in terms of radius value):
pbond #1.34:940@O #1.34:472@O reveal true color red dashes 0 radius 0.7 pbond #1.34:368@O #1.34:1044@O reveal true color red dashes 10 radius 0.5
I haven't tried yet to call these 2 pbonds from 2 different models to see if I can trick this representation.
Generally, it would be useful to be able to show different kinds of argument per model, the figures are getting more complex now I feel. I'm managing to reach this by loading several time the same model and only showing the parts I'm interesting in but the script gets very messy and long, while if we can only load 1 model and modify it the way we want it would make it easier and cleaner.
Thanks Vincent
Le 10/12/2024 à 17:57, Elaine Meng a écrit :
Hi Vincent, The "pbond" command is only in version 1.8 or newer, according to the Change Log. Maybe what you have is too old, so get a newer ChimeraX. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>
What you said should work if those atoms actually exist and the model is not hidden. Similar commands work just fine for me, e.g.
open 2gbp pbond #1/A:13@O #1/A:153@O reveal true color magenta dashes 1 cartoon suppress false
("cartoon suppress false" allows showing backbone atoms at same time as cartoon)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 10, 2024, at 6:38 AM, Vincent CHAPTAL via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model.
I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands.
I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0
but the distance does not appear on my screen.
Could you help me work this out? Thank you Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
_______________________________________________ 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/
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
_______________________________________________ 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/
participants (3)
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Elaine Meng -
Vincent CHAPTAL -
Vincent Chaptal