CA atoms connected by tether when trying to show sidechains only in a model
Hello,
I am trying to show only sidechains in one model, so I can compare rotamers with another model where I am displaying cartoon and sidechains. However, when I display sidechains using the sidechain selector (e.g. "show #1 & sidechain") the CA atoms become linked by tethers.
[cid:image001.png@01DA4F98.8C977390]
How can I suppress this display? I can see its possible to suppress tethers between cartoon helices and a sidechain in the same model but that doesn't seem to apply here as I'm not showing the cartoon at all in the models where the CA tethers are present.
KR, Sam
Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom
The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.
Hi Sam, I don't think those are tethers (which only connect sidechains to ribbon, not atoms to atoms), but instead long bonds from autochaining CA atoms of adjacent residues. Some people like to show a CA-only chain, which is why this autochaining exists, but you can turn it off as described below.
Also "sidechain" includes CA since most people don't want them detached from the ribbon -- you would instead use "sideonly" to exclude CA. These selectors are explained here: https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin
I can't remember if autochaining will also connect other atoms, but If you try sideonly and still see those long bonds, you could also try the following command to turn off autochaining:
setattr m autochain false
The "setattr" command changes attribute values, "m" means attribute of models, "autochain" is the name of the specific attribute. https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html
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 Jan 25, 2024, at 6:12 AM, Samuel Haysom via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I am trying to show only sidechains in one model, so I can compare rotamers with another model where I am displaying cartoon and sidechains. However, when I display sidechains using the sidechain selector (e.g. “show #1 & sidechain”) the CA atoms become linked by tethers.
<image001.png>
How can I suppress this display? I can see its possible to suppress tethers between cartoon helices and a sidechain in the same model but that doesn’t seem to apply here as I’m not showing the cartoon at all in the models where the CA tethers are present.
KR, Sam
As Elaine mentioned the C-alpha atoms are connected by a chain trace. Another way to hide that is if you click on the ">" to the left of your model the Models panel it will show submodels and one will be named "chain trace" and you can click the hide checkbutton next to that (under the eye icon).
Tom
On Jan 25, 2024, at 6:12 AM, Samuel Haysom via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I am trying to show only sidechains in one model, so I can compare rotamers with another model where I am displaying cartoon and sidechains. However, when I display sidechains using the sidechain selector (e.g. “show #1 & sidechain”) the CA atoms become linked by tethers.
<image001.png>
How can I suppress this display? I can see its possible to suppress tethers between cartoon helices and a sidechain in the same model but that doesn’t seem to apply here as I’m not showing the cartoon at all in the models where the CA tethers are present.
KR, Sam Samuel Haysom mailto:Samuel.Haysom@soseiheptares.com | Research Scientist | Biophysics Sosei Heptares https://soseiheptares.com/ | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom
The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.
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participants (3)
-
Elaine Meng -
Samuel Haysom -
Tom Goddard