I cant get my named selections to work. Here is an example. select #1/V:80@CD2 1 atom, 1 residue, 1 model selected name test sel select clear select test Nothing selected - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation
You need to use name frozen test sel which will set test to be the currently selected atoms. In your example you used name test sel which just sets the name test to be the name "sel". So later when you use it uses "sel" and since nothing is selected. This "name frozen" versus "name" command is confusing. Tom
On Jan 22, 2026, at 5:21 PM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I cant get my named selections to work. Here is an example. select <> #1/V:80@CD2 1 atom, 1 residue, 1 model selected name <> test sel select clear <> select <> test Nothing selected
- Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation _______________________________________________ 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/
Think of "name" (without frozen) as simple text substitution, whereas "name frozen" will specify a frozen set of atoms, those that were specified at the time the name was given. So if you do this open 1zik name blah1 protein name frozen blah2 protein open 4hhb ... "blah1" will specify all the protein(s) that are currently open since it is identical to substituting in the text "protein", whereas "blah2" will only specify the protein in 1zik, because that was the only protein open when the "name frozen" command was issued. 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 22, 2026, at 5:36 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
You need to use
name frozen test sel
which will set test to be the currently selected atoms. In your example you used
name test sel
which just sets the name test to be the name "sel". So later when you use it uses "sel" and since nothing is selected. This "name frozen" versus "name" command is confusing.
Tom
On Jan 22, 2026, at 5:21 PM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I cant get my named selections to work. Here is an example. select #1/V:80@CD2 1 atom, 1 residue, 1 model selected name test sel select clear select test Nothing selected
- Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation
Thanks! The other thing that happens to me is that I use the cd command to specify my directory in a .cxc script. Each time I load a protein it confirms that directory. But then it later defaults to my home directory. - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation On Thu, Jan 22, 2026 at 8:53 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Think of "name" (without frozen) as simple text substitution, whereas "name frozen" will specify a frozen set of atoms, those that were specified at the time the name was given.
So if you do this
open 1zik name blah1 protein name frozen blah2 protein open 4hhb
... "blah1" will specify all the protein(s) that are currently open since it is identical to substituting in the text "protein", whereas "blah2" will only specify the protein in 1zik, because that was the only protein open when the "name frozen" command was issued.
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 22, 2026, at 5:36 PM, Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
You need to use
name frozen test sel
which will set test to be the currently selected atoms. In your example you used
name test sel
which just sets the name test to be the name "sel". So later when you use it uses "sel" and since nothing is selected. This "name frozen" versus "name" command is confusing.
Tom
On Jan 22, 2026, at 5:21 PM, Timothy Springer via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
I cant get my named selections to work. Here is an example. select #1/V:80@CD2 1 atom, 1 residue, 1 model selected name test sel select clear select test Nothing selected
- Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation
Hi Tim, When you open a ChimeraX command script (.cxc file) it automatically changes directory to the directory of the script, and when the script ends automatically changes the directory back to the original directory ChimeraX was in. This is described in the documentation here https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#... "Working directory: Opening a command file changes the current directory to the directory containing that file. After execution of the file finishes, the current directory is changed back to what it was previously. See also: cd" Tom
On Jan 23, 2026, at 7:50 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks! The other thing that happens to me is that I use the cd command to specify my directory in a .cxc script. Each time I load a protein it confirms that directory. But then it later defaults to my home directory. - Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation
On Thu, Jan 22, 2026 at 8:53 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Think of "name" (without frozen) as simple text substitution, whereas "name frozen" will specify a frozen set of atoms, those that were specified at the time the name was given.
So if you do this
open 1zik name blah1 protein name frozen blah2 protein open 4hhb
... "blah1" will specify all the protein(s) that are currently open since it is identical to substituting in the text "protein", whereas "blah2" will only specify the protein in 1zik, because that was the only protein open when the "name frozen" command was issued.
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 22, 2026, at 5:36 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
You need to use
name frozen test sel
which will set test to be the currently selected atoms. In your example you used
name test sel
which just sets the name test to be the name "sel". So later when you use it uses "sel" and since nothing is selected. This "name frozen" versus "name" command is confusing.
Tom
On Jan 22, 2026, at 5:21 PM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
I cant get my named selections to work. Here is an example. select #1/V:80@CD2 1 atom, 1 residue, 1 model selected name test sel select clear select test Nothing selected
- Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation
_______________________________________________ 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/
If you want to have ChimeraX be in a specific directory when it starts up, you could put the needed 'cd' command in the commands that ChimeraX executes at startup. You can find those in the "Startup" section of the ChimeraX preferences. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 23, 2026, at 10:10 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tim,
When you open a ChimeraX command script (.cxc file) it automatically changes directory to the directory of the script, and when the script ends automatically changes the directory back to the original directory ChimeraX was in. This is described in the documentation here
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#...
"Working directory: Opening a command file changes the current directory to the directory containing that file. After execution of the file finishes, the current directory is changed back to what it was previously. See also: cd"
Tom
On Jan 23, 2026, at 7:50 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks! The other thing that happens to me is that I use the cd command to specify my directory in a .cxc script. Each time I load a protein it confirms that directory. But then it later defaults to my home directory. - Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation
On Thu, Jan 22, 2026 at 8:53 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Think of "name" (without frozen) as simple text substitution, whereas "name frozen" will specify a frozen set of atoms, those that were specified at the time the name was given.
So if you do this
open 1zik name blah1 protein name frozen blah2 protein open 4hhb
... "blah1" will specify all the protein(s) that are currently open since it is identical to substituting in the text "protein", whereas "blah2" will only specify the protein in 1zik, because that was the only protein open when the "name frozen" command was issued.
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 22, 2026, at 5:36 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
You need to use
name frozen test sel
which will set test to be the currently selected atoms. In your example you used
name test sel
which just sets the name test to be the name "sel". So later when you use it uses "sel" and since nothing is selected. This "name frozen" versus "name" command is confusing.
Tom
On Jan 22, 2026, at 5:21 PM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
I cant get my named selections to work. Here is an example. select #1/V:80@CD2 1 atom, 1 residue, 1 model selected name test sel select clear select test Nothing selected
- Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation
_______________________________________________ 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/
_______________________________________________ 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/
participants (4)
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Elaine Meng -
Eric Pettersen -
Timothy Springer -
Tom Goddard