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/

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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/