[chimerax-users] [Ext] Re: Display chain annotations w/o having to reopen files

[Alexander Julian]

Thank you so much, Eric!

I appreciate your help!

On Wed, Apr 28, 2021 at 3:35 PM Eric Pettersen <pett at 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 at 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 at 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 at 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 at 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 at 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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