Hi George,
A mild goof, but easy to miss:

open ~Desktop/ChimeraX_test/delta_1PN9.pdb

should be:

open ~/Desktop/ChimeraX_test/delta_1PN9.pdb

Note the '/' between '~' and 'Desktop'.

--Eric

On Oct 28, 2025, at 11:44 AM, George Tzotzos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Many thanks Eric for the prompt reply
I set up a test directory
ls /Users/george/Desktop/ChimeraX_test 
color_delta_epsilon_divergence.cxc delta_kd.defattr
color_delta_epsilon_kdshift.cxc epsilon_2IMI.pdb
delta_1PN9.pdb epsilon_div.defattr
delta_div.defattr epsilon_kd.defattr

I have renamed the files as per your suggestion. I get:
open /Users/george/Desktop/ChimeraX_test/color_delta_epsilon_divergence.cxc
open ~Desktop/ChimeraX_test/delta_1PN9.pdb
No such file/path: ~Desktop/ChimeraX_test/delta_1PN9.pdb

Have I goofed somewhere else?

George
On 28 Oct 2025, at 17:22, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi George,
A ChimeraX command script file needs to have a suffix of .cxc .  Yours has a suffix of .cxs (which is the suffix for ChimeraX session files).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Oct 28, 2025, at 10:09 AM, George Tzotzos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I’d be grateful for your help

My script is:
# Auto-generated by make_chimerax_assets.py
# Visualize L1 composition divergence on delta (1PN9) and epsilon (2IMI)
open viz/delta_1PN9.pdb
open viz/epsilon_2IMI.pdb
defattr viz/delta_div.defattr model #1
defattr viz/epsilon_div.defattr model #2
style #1,#2 cartoon
cartoon smoothRibbon true
color byattribute divergence palette bluesred range 0,1 #1
color byattribute divergence palette bluesred range 0,1 #2
key colorbar palette bluesred range 0,1 label "Δ composition (L1)" pos 0.85,0.15 size 0.03,0.5
lighting soft
zoom true

When I try to open the color_delta_epsilon_divergence.cxs (see above), I get:
RuntimeError: Not a ChimeraX session file

File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 798, in restore
raise RuntimeError("Not a ChimeraX session file”)

Thank you
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