I see. thanks again. On Mon, May 8, 2023 at 3:55 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Yes, as I tried to explain before, the ribbon suppresses the backbone atom display, so it doesn't make a difference when the ribbon is shown. If you hide the ribbon, it will reveal whether the backbone atoms are also shown or not. Best, Elaine
On May 8, 2023, at 3:49 PM, James Raymond via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
thank you. I used your commands to show these 3 Thr sidechains Adding "& sidechain" didn't seem to make a difference.
<image.png>
On Mon, May 8, 2023 at 2:38 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi James, You're welcome!
I was guessing that you were already showing ribbons, which (by default) prevents displaying backbone atoms at the same time, so that the commands I gave would show the sidechain in addition to the existing ribbon representation of the backbone. If you weren't showing the ribbon, the example commands I gave would show all of the atoms of the whole residue.
If the ribbon wasn't shown and you really wanted to show only the side chain atoms of the residue and NOT the backbone atoms, you would use the option to show side chain only.
That option appears in the Actions menu as in the image you just sent, or you can use the command-line specifier "sidechain" (includes CA atom) or "sideonly" (does not include CA atom) explained in the atomspec page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin
...for example intersecting the "sidechain" specification with the chain and residue number specification:
show /A:10 & sidechain
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 8, 2023, at 2:03 PM, James Raymond via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, thank you so much. it worked. I got bogged down in instructions that made me think I had to use "sidechain" or "side chain" in the command, and all I got was errors. JIm <image.png>
On Mon, May 8, 2023 at 1:29 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi James, There are lots of ways to do it, but here is the command to show all atoms of residue 10 in chain A of model #1:
show #1/A:10
You can be less specific, e.g.:
show /A:10
...meaning display residue 10 of chain A in all models (and maybe you only have one anyway)
show :10
...meaning display residue 10 in all chains and all models that have a residue 10
All of the command help pages include a usage line showing how to use the command, where "atom-spec" in the usage line links to this other page that explains all of the stuff I said above, and more (e.g. you could also use residue name, atomic element symbol, ...), including several examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
You can also click the link from the word "Usage" which explains the conventions in the command usage information. Once you understand the usage of the command, it is pretty simple, as all the options will be explained in the help.
There are also many example commands in the tutorials <https://www.rbvi.ucsf.edu/chimerax/tutorials.html>
... for example, protein-ligand binding sites < https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> ... delta-opioid receptor ligand bindin < https://www.rbvi.ucsf.edu/chimerax/data/delta-opioid-jan2020/binding.html>
It is hard to answer a basic question like this completely because there are so many other ways to do it, however. For example, you could show the sequence of the protein and select the residue from there, or Ctrl-click on its ribbon segment in the graphics window to select it, and then use the Actions menu to show the atoms, or instead of the Actions menu, you could use the icon for atom display in the toolbar across the top.
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 8, 2023, at 1:02 PM, James Raymond via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
I am having trouble understanding the manual. I wish to show the side chain for a particular amino acid in my protein. What is the command line to do this?
thank you James Raymond
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