Transparency for atoms selected only
Hello, I am trying to display transparency only for selected residues in my protein model but I am having a hard time trying to restrict the transparency only to the selected set of atoms (it sets the transparency to all residues). Do you have any suggestions and/or examples about this? Thanks, Gabriele
Hi Gabriele, It would be useful to give more detail on what exactly you tried and what you want. I don't know if you were using the menu, or the "color" command, or the "transparency" command and whether you mean the atomic representation (sticks, balls, ...), ribbons, and/or molecular surface. However, here is an example of changing the transparency of the atomic representation of selected atoms only, using the transparency command and a value of 70%. Example commands: open 2gbp select ligand transparency sel 70 target a You can use command "help transparency" to show the help page for the command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> In commands, you use "sel" to mean the selected atoms. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> The Actions menu automatically applies to the selected parts, but it does not have an option for changing transparency of atomic representations. 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 20, 2020, at 4:02 PM, Gabriele Cerutti <gc2695@columbia.edu> wrote:
Hello, I am trying to display transparency only for selected residues in my protein model but I am having a hard time trying to restrict the transparency only to the selected set of atoms (it sets the transparency to all residues). Do you have any suggestions and/or examples about this? Thanks, Gabriele
Hi Elaine, That's exactly what I needed: transparency sel 70 target a I was not able to put the "sel" specifier in the right place, and I had a hard time trying to find the solution in the documentation. Thanks for your prompt response! Best, Gabriele On Fri, Nov 20, 2020 at 7:12 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gabriele, It would be useful to give more detail on what exactly you tried and what you want. I don't know if you were using the menu, or the "color" command, or the "transparency" command and whether you mean the atomic representation (sticks, balls, ...), ribbons, and/or molecular surface.
However, here is an example of changing the transparency of the atomic representation of selected atoms only, using the transparency command and a value of 70%. Example commands:
open 2gbp select ligand transparency sel 70 target a
You can use command "help transparency" to show the help page for the command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>
In commands, you use "sel" to mean the selected atoms. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
The Actions menu automatically applies to the selected parts, but it does not have an option for changing transparency of atomic representations.
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 20, 2020, at 4:02 PM, Gabriele Cerutti <gc2695@columbia.edu> wrote:
Hello, I am trying to display transparency only for selected residues in my protein model but I am having a hard time trying to restrict the transparency only to the selected set of atoms (it sets the transparency to all residues). Do you have any suggestions and/or examples about this? Thanks, Gabriele
Hi Gabriele, You're welcome! In the "Usage" lines in the command help pages, where it says "spec" or "atom-spec" is where you put the specifier of which atoms, residues, models to act upon. Usually "spec" or "atom-spec" is a link that goes to this page explaining the many ways to specify, including the word "sel" which means the current selection: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Best, Elaine
On Nov 20, 2020, at 6:58 PM, Gabriele Cerutti <gc2695@columbia.edu> wrote:
Hi Elaine, That's exactly what I needed:
transparency sel 70 target a
I was not able to put the "sel" specifier in the right place, and I had a hard time trying to find the solution in the documentation. Thanks for your prompt response! Best,
Gabriele
On Fri, Nov 20, 2020 at 7:12 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Gabriele, It would be useful to give more detail on what exactly you tried and what you want. I don't know if you were using the menu, or the "color" command, or the "transparency" command and whether you mean the atomic representation (sticks, balls, ...), ribbons, and/or molecular surface.
However, here is an example of changing the transparency of the atomic representation of selected atoms only, using the transparency command and a value of 70%. Example commands:
open 2gbp select ligand transparency sel 70 target a
You can use command "help transparency" to show the help page for the command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>
In commands, you use "sel" to mean the selected atoms. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
The Actions menu automatically applies to the selected parts, but it does not have an option for changing transparency of atomic representations.
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 20, 2020, at 4:02 PM, Gabriele Cerutti <gc2695@columbia.edu> wrote:
Hello, I am trying to display transparency only for selected residues in my protein model but I am having a hard time trying to restrict the transparency only to the selected set of atoms (it sets the transparency to all residues). Do you have any suggestions and/or examples about this? Thanks, Gabriele
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participants (2)
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Elaine Meng -
Gabriele Cerutti