[chimerax-users] Cartoon “Highlight color” and “Suppress false” Feature

[Elaine Meng]

Hi Arun,
Your wording was reasonable except that I don't use Pymol, so I didn't know what "highlight color" means in Pymol... the link to a picture is helpful.  Now I can see that you mean something like the Chimera "ribbon inside color" for helices.

Sorry no, ChimeraX does not have an option to use a different color inside of helix ribbons.  Only Chimera has this option.

As for "cartoon suppress false", at least in my tests, it also works fine to use it before "show":

open 1g1p
cartoon suppress false
show :1-5 at n,ca,c,o

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 12, 2022, at 7:13 AM, Gupta, Arun via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello Elaine,
> 
> Thanks for your reply. Now, I know what was going wrong in my script for NMR ensemble models. I was giving the "cartoon suppress false " command before  the "show " command. 
> 
> My wording was probably wrong which might have confused you. Actually, I was interested to know whether  the following "Cartoon highlight color" feature has been  updated in the newer version of the ChimeraX ?
> 
> https://pymolwiki.org/index.php/Cartoon_highlight_color
> Cartoon highlight color - PyMOLWiki
> Overview. This setting allows one to specify a contrasting color for the interior face of helices and the side faces of strands. Settings
> pymolwiki.org
> 
> Thanks & Regards
> Arun
> 
> Arun Gupta PhD, MRSC
> Research Fellow
> Challis & Lewandowski Group
> Chemistry Department
> University of Warwick
> Gibbet Hill Road
> Coventry CV4 7AL
> United Kingdom
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, May 10, 2022 5:50 PM
> To: Gupta, Arun <Arun.Gupta at warwick.ac.uk>
> Cc: ChimeraX-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Cartoon “Highlight color” and “Suppress false” Feature
>  
> Hello Arun,
> There is nothing called "Pymol Cartoon highlight color" in ChimeraX, but maybe if you explain what it is, you can do the same coloring in ChimeraX.
> 
> "cartoon suppress false" works fine for me on NMR models, but be advised that it does not turn on the display of the backbone atoms... you still have to display the ones you actually want to show.  E.g.
> 
> open 1g1p
> show :1-5 at n,ca,c,o
> cartoon suppress false
> tile 
> undo
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On May 10, 2022, at 8:53 AM, Gupta, Arun via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hello ChimeraX team,  
> > I am just wondering whether the “Pymol Cartoon highlight color” feature of helix and strand has been brought in the newer or the daily build versions of the ChimeraX. Someone has been just recently verbally referring to me that this feature has been updated in the newer versions of ChimeraX, but I couldn’t locate the mention in the ChimeraX mailing list.  
> >  
> > Also, I have noticed that “cartoon suppress false” command doesn’t work for the NMR ensemble PDBs I think it's more to do with specifying the “cartoon suppress false” command for the individual PDB model within ensemble PDBs. I did try to play around with selection notation for individual model with “cartoon suppress false” command but couldn’t get it right.  Can you please specify the exact command notation to work around with NMR ensemble PDBs  
> > Thanks!    
> > Arun