Re: [chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files?
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@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@cgl.ucsf.edu <mailto:chimerax-users@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@salilab.org <mailto:ben@salilab.org>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Reply-To: Tom Goddard <goddard@sonic.net <mailto:goddard@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>
On 11/12/21 3:14 PM, Tom Goddard wrote:
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.
I've never used the ModBase fetch capability in Chimera - after all, my job is to put models into ModBase, not to take them out! - but if you were to add it I'd recommend you fetch as mmCIF rather than PDB. IMHO parsing the new mmCIF tables would be the more desirable feature because it isn't limited to ModBase models - and as Tom says, would work regardless of how you get the file. Ben -- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
participants (2)
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Ben Webb -
Tom Goddard