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

[Alexander Julian]

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 at 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 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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