Re: [ccpem] Making thioester bond in Chimera/ChimeraX
Hi Firdous, No trick, it is an option of cartoon (on by default) to prevent showing backbone atoms at the same time. Glycine only has backbone atoms (no sidechain). If you really want to show cartoon and backbone atoms at the same, use
cartoon suppress false
This is explained in the "cartoon" or "ribbon" command help. Just type command "help cartoon" to see your downloaded copy of the help page, or see the copy on our website here:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html
The full name of the option is "suppressBackboneDisplay" but you can shorten all options in commands as long as there is no other option that starts with the same letters.
Actually Chimera ribbon also hides backbone atoms by default, although you can allow showing both at the same time with the Chimera "ribbackbone" command.
The best address to use for ChimeraX questions is the chimerax-users one that I CC'd on this message, unless you are including data that must be kept private.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 13, 2023, at 2:59 PM, Firdous Tarique kahkashantarique@gmail.com wrote:
Hi Elaine
Now I know where the problem is. 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 structure 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). However this is not the case in Pymol and Chimera. Do you know any tricks to fix that in ChimeraX?
Best
Firdous
On Thu, Nov 9, 2023 at 6:11 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hello Firdous, Probably the problem is that mol A and mol B are two different models. You can't add a bond in Chimera or ChimeraX until after combining them into one model first.
ChimeraX combine command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html
ChimeraX bond command or Build Structure tool, Adjust Bonds section: https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds
For the best chance of getting an answer to a question about ChimeraX, please use the chimerax-users@cgl.ucsf.edu address: https://rbvi.ucsf.edu/chimerax/docs/contact.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: Collaborative Computational Project in Electron cryo-Microscopy CCPEM@JISCMAIL.AC.UK on behalf of Firdous Tarique kahkashantarique@GMAIL.COM Date: Thursday, November 9, 2023 at 12:27 PM To: CCPEM@JISCMAIL.AC.UK CCPEM@JISCMAIL.AC.UK Subject: [ccpem] Making thioester bond in Chimera/ChimeraX
Hi
Does anybody know how to make thioester bonds in Chimera or ChimeraX ?
I am unable to make a bond between Cys321 in mol A with Gly1 in mol B (S-glycyl-L-cysteine) using Chimera or ChimeraX.
I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond between selected atoms but so far have been unsuccessful. I don't know if I am missing something.
Any help would be appreciated.
Thanks
Firdous
To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
Just to clarify: After enabling backbone atom display at the same time as cartoon with "cartoon suppress false", you may still need to display the atoms of interest, e.g. if your glycine is residue 54 of chain A,
show /A:54
Simply enabling backbone-atom display at the same time as cartoon does not automatically display all of the backbone atoms, since one might not want that. Best, Elaine
On Nov 13, 2023, at 3:21 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Firdous, No trick, it is an option of cartoon (on by default) to prevent showing backbone atoms at the same time. Glycine only has backbone atoms (no sidechain). If you really want to show cartoon and backbone atoms at the same, use
cartoon suppress false
This is explained in the "cartoon" or "ribbon" command help. Just type command "help cartoon" to see your downloaded copy of the help page, or see the copy on our website here:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html
The full name of the option is "suppressBackboneDisplay" but you can shorten all options in commands as long as there is no other option that starts with the same letters.
Actually Chimera ribbon also hides backbone atoms by default, although you can allow showing both at the same time with the Chimera "ribbackbone" command.
The best address to use for ChimeraX questions is the chimerax-users one that I CC'd on this message, unless you are including data that must be kept private.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 13, 2023, at 2:59 PM, Firdous Tarique kahkashantarique@gmail.com wrote:
Hi Elaine
Now I know where the problem is. 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 structure 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). However this is not the case in Pymol and Chimera. Do you know any tricks to fix that in ChimeraX?
Best
Firdous
On Thu, Nov 9, 2023 at 6:11 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hello Firdous, Probably the problem is that mol A and mol B are two different models. You can't add a bond in Chimera or ChimeraX until after combining them into one model first.
ChimeraX combine command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html
ChimeraX bond command or Build Structure tool, Adjust Bonds section: https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds
For the best chance of getting an answer to a question about ChimeraX, please use the chimerax-users@cgl.ucsf.edu address: https://rbvi.ucsf.edu/chimerax/docs/contact.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: Collaborative Computational Project in Electron cryo-Microscopy CCPEM@JISCMAIL.AC.UK on behalf of Firdous Tarique kahkashantarique@GMAIL.COM Date: Thursday, November 9, 2023 at 12:27 PM To: CCPEM@JISCMAIL.AC.UK CCPEM@JISCMAIL.AC.UK Subject: [ccpem] Making thioester bond in Chimera/ChimeraX
Hi
Does anybody know how to make thioester bonds in Chimera or ChimeraX ?
I am unable to make a bond between Cys321 in mol A with Gly1 in mol B (S-glycyl-L-cysteine) using Chimera or ChimeraX.
I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond between selected atoms but so far have been unsuccessful. I don't know if I am missing something.
Any help would be appreciated.
Thanks
Firdous
To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
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
Thanks a lot. 'cartoon suppress false' worked for me.
Best wishes
Firdous
On Mon, Nov 13, 2023 at 5:21 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Firdous, No trick, it is an option of cartoon (on by default) to prevent showing backbone atoms at the same time. Glycine only has backbone atoms (no sidechain). If you really want to show cartoon and backbone atoms at the same, use
cartoon suppress false
This is explained in the "cartoon" or "ribbon" command help. Just type command "help cartoon" to see your downloaded copy of the help page, or see the copy on our website here:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html
The full name of the option is "suppressBackboneDisplay" but you can shorten all options in commands as long as there is no other option that starts with the same letters.
Actually Chimera ribbon also hides backbone atoms by default, although you can allow showing both at the same time with the Chimera "ribbackbone" command.
The best address to use for ChimeraX questions is the chimerax-users one that I CC'd on this message, unless you are including data that must be kept private.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 13, 2023, at 2:59 PM, Firdous Tarique kahkashantarique@gmail.com
wrote:
Hi Elaine
Now I know where the problem is. 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 structure 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). However this is not the case in Pymol and Chimera. Do you know any tricks to fix that in ChimeraX?
Best
Firdous
On Thu, Nov 9, 2023 at 6:11 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hello Firdous, Probably the problem is that mol A and mol B are two different models.
You can't add a bond in Chimera or ChimeraX until after combining them into one model first.
ChimeraX combine command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html
ChimeraX bond command or Build Structure tool, Adjust Bonds section: https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html <
https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds%3E
For the best chance of getting an answer to a question about ChimeraX,
please use the chimerax-users@cgl.ucsf.edu address:
https://rbvi.ucsf.edu/chimerax/docs/contact.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: Collaborative Computational Project in Electron cryo-Microscopy <
CCPEM@JISCMAIL.AC.UK> on behalf of Firdous Tarique < kahkashantarique@GMAIL.COM>
Date: Thursday, November 9, 2023 at 12:27 PM To: CCPEM@JISCMAIL.AC.UK CCPEM@JISCMAIL.AC.UK Subject: [ccpem] Making thioester bond in Chimera/ChimeraX
Hi
Does anybody know how to make thioester bonds in Chimera or ChimeraX ?
I am unable to make a bond between Cys321 in mol A with Gly1 in mol B
(S-glycyl-L-cysteine) using Chimera or ChimeraX.
I tried Isolde in ChimeraX and Build Structure in Chimera to make a
bond between selected atoms but so far have been unsuccessful. I don't know if I am missing something.
Any help would be appreciated.
Thanks
Firdous
To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
participants (2)
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Elaine Meng -
Firdous Tarique