[chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files?

[Tom Goddard]

Hi Elaine,

This is related but a little different from what Ben was asking.  It is different because the template and scoring data in the mmCIF tables could be shown no matter how the mmCIF file is loaded -- it would not be limited to fetching from ModBase.

Maybe Ben has an opinion about how desirable it is to put the Chimera ModBase fetch capability into ChimeraX, and whether it is more or less desirable than making the new mmCIF tables accessible in ChimeraX, to help figure out priorities.

	Tom

> On Nov 12, 2021, at 3:05 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Chimera had a ModBase Fetch:  
> 
> "a SwissProt, TrEMBL, GenPept or PIR accession code will be used to fetch comparative models in PDB format from ModBase (associated information will be shown in a model list)"
> 
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html>
> 
> ...where "model list" is the same dialog as used to show Modeller results.  Now that ChimeraX has a Modeller Results dialog for displaying the output from Comparative Modeling and Model Loops, could consider adding analogous Modbase fetch capability.
> 
> I can make a ticket if anybody thinks that's a good idea.
> 
> Elaine
> 
> 
>> Begin forwarded message:
>> 
>> From: Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
>> Subject: Re: [chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files?
>> Date: November 12, 2021 at 2:56:49 PM PST
>> To: Ben Webb <ben at salilab.org <mailto:ben at salilab.org>>
>> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
>> Reply-To: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
>> 
>> 
>>   So it looks like only ModBase would currently benefit from ChimeraX reading template sequences and alignments.  I do not think it would be too hard to implement it.  I've made a ChimeraX feature request for that
>> 
>> 	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5601 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5601>

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