Cartoon “Highlight color” and “Suppress false” Feature
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 Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom
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@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@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
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<https://pymolwiki.org/index.php/Cartoon_highlight_color> 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@cgl.ucsf.edu> Sent: Tuesday, May 10, 2022 5:50 PM To: Gupta, Arun <Arun.Gupta@warwick.ac.uk> Cc: ChimeraX-users@cgl.ucsf.edu <chimerax-users@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@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@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
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@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@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@cgl.ucsf.edu> Sent: Tuesday, May 10, 2022 5:50 PM To: Gupta, Arun <Arun.Gupta@warwick.ac.uk> Cc: ChimeraX-users@cgl.ucsf.edu <chimerax-users@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@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@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
participants (2)
-
Elaine Meng -
Gupta, Arun