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