On Apr 28, 2021, at 2:45 PM, Alexander Julian <ajulian@hawk.iit.edu> wrote:

I've implemented the code and ran it as you suggested, however the output for the chain description is 'No description available' for each structure.

On Wed, Apr 28, 2021 at 3:48 PM Alexander Julian <ajulian@hawk.iit.edu> wrote:

Thank you so much, Eric!

I appreciate your help!

On Wed, Apr 28, 2021 at 3:35 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:

No, as long as you're using --nogui (which it certainly sounds like you should be here) the Log tool will not be started and therefore will have no saved state to restore when the session gets restored.  As a hack until that enhancement ticket gets implemented you can force the chain table into the log (after the session is restored) with this code:

from chimerax.atomic import Structure

for m in session.models:

if isinstance(m, Structure):

m._report_chain_descriptions(session)

You could put that in a .py file and use 'open' to run it.  As an additional hack, you can pretend it's a "preset" and add it to the Presets menu (see Presets→Add A Preset...) so you can easily execute it using that menu.

--Eric

On Apr 28, 2021, at 12:56 PM, Alexander Julian <ajulian@hawk.iit.edu> wrote:

I am currently running with --nogui because I'm running an automated process. Would running --offscreen resolve this issue? 

On Wed, Apr 28, 2021, 2:54 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Well, whatever the contents of Log tool was when the session was saved should be restored.  If there was no Log tool (for instance, if this script creates sessions in "nogui" mode) then nothing is restored.

--Eric

On Apr 28, 2021, at 12:42 PM, Alexander Julian <ajulian@hawk.iit.edu> wrote:

I am not sure of the exact release version, but it is has definitely been installed this year.

I create the sessions using a python script and open it with the command line, does that prevent the session messages from restoring? 

On Wed, Apr 28, 2021, 1:49 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Alexander,

There is no command to re-show the chain table.  I have added you to the recipient list for the enhancement-request ticket we have open for that.

Nonetheless, the chain table should still be in the log contents after the session is restored.  At least for sessions saved in versions of ChimeraX since March of 2020, when that capability was added.  Are you using an old version of ChimeraX?

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Apr 27, 2021, at 3:19 PM, Alexander Julian <ajulian@hawk.iit.edu> wrote:

Good afternoon,

I was wondering if there was any built-in functionality to show the chain annotations that are shown when the file is first open?

When I save a session (.cxs) and reopen it later, this information is missing.

Best,

Alexander

--

Alexander T. Julian

PhD Student, Department of Biology, Microbiology

Bachelor of Science, Biomedical Engineering, Cell and Tissue Specialization 2021

Master of Advanced Study, Chemical Engineering 2021

Illinois Institute of Technology

Chicago, IL 60616

Phone (727)-735-7104

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