Hi everyone
In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any of the structures if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that).
My aim is to show the thioester bond between Gly and Cys of two chains which I am able to create in Coot through Molecule Link but not able to see in ChimeraX. The moment I am trying to show Gly in stick form at this position it breaks the cartoon. I realised that this is for all the Glycines in the structure. Showing stick and cartoon together shows all amino acids in the stick except Glycine. (However this is not the case in Pymol and Chimera).
Do you know any tricks to fix that in ChimeraX?
Best
Firdous
Hi Firdous! You probably saw the previous answer to this question, link below:
I sent that answer earlier since I didn't realize you also mailed your question to this chimerax-users address. Thanks for doing that! It is easier for us to keep track of questions that way. Usually the incoming questions are moderated quickly, or if you want to skip moderation in the future (and see other answers) you can sign up to be a member of the list:
https://www.rbvi.ucsf.edu/chimerax/docs/contact.html https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimerax-users.cgl.ucsf.edu/
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 13, 2023, at 3:06 PM, Firdous Tarique via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi everyone
In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any of the structures if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that).
My aim is to show the thioester bond between Gly and Cys of two chains which I am able to create in Coot through Molecule Link but not able to see in ChimeraX. The moment I am trying to show Gly in stick form at this position it breaks the cartoon. I realised that this is for all the Glycines in the structure. Showing stick and cartoon together shows all amino acids in the stick except Glycine. (However this is not the case in Pymol and Chimera).
Do you know any tricks to fix that in ChimeraX?
Best
Firdous
Hi Elaine
I will subscribe to this mailing list. Earlier I posted the question on different forum after I saw my ChimeraX email went for moderator's evaluation, I thought that now it will take lots of time and I was in hurry.
But your input actually solved my problem.
Best regards
Firdous
On Mon, 13 Nov 2023, 18:50 Elaine Meng, meng@cgl.ucsf.edu wrote:
Hi Firdous! You probably saw the previous answer to this question, link below:
< https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...
I sent that answer earlier since I didn't realize you also mailed your question to this chimerax-users address. Thanks for doing that! It is easier for us to keep track of questions that way. Usually the incoming questions are moderated quickly, or if you want to skip moderation in the future (and see other answers) you can sign up to be a member of the list:
https://www.rbvi.ucsf.edu/chimerax/docs/contact.html < https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimerax-users.cgl.ucsf.edu...
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 13, 2023, at 3:06 PM, Firdous Tarique via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone
In ChimeraX I am not able to show Gly simultaneously as a stick and
cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any of the structures if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that).
My aim is to show the thioester bond between Gly and Cys of two chains
which I am able to create in Coot through Molecule Link but not able to see in ChimeraX. The moment I am trying to show Gly in stick form at this position it breaks the cartoon. I realised that this is for all the Glycines in the structure. Showing stick and cartoon together shows all amino acids in the stick except Glycine. (However this is not the case in Pymol and Chimera).
Do you know any tricks to fix that in ChimeraX?
Best
Firdous
participants (2)
-
Elaine Meng -
Firdous Tarique