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

[Alexander Julian]

We've all been there before :-) I really appreciate the help

On Wed, Apr 28, 2021, 6:21 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Oops!  I told you it was a hack. :-)
>
> Above the line
>
> *m._report_chain_descriptions(session)*
>
> add:
>
> *m._set_chain_descriptions(session)*
>
> --Eric
>
> On Apr 28, 2021, at 2:45 PM, Alexander Julian <ajulian at 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 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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