Changes between Version 29 and Version 30 of NIAID2024


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Timestamp:
Sep 26, 2024, 2:26:34 PM (13 months ago)
Author:
Elaine Meng
Comment:

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  • NIAID2024

    v29 v30  
    9797Darrell asks about user base of ChimeraX.  Elaine: cryoEM people are most of the cutting-edge papers, but we also have a significant number of general molecular modeling people, especially recently for viewing !AlphaFold predictions.  Eric: we are more dominant in cryoEM, as there is more competition for general molecular modeling.  Darrell: Pymol can be obtained in packages instead of a download from a website, any developments along those lines? Zach: Greg and I were working on changing licensing to agreement upon first use rather than at download, which would then enable different ways of getting ChimeraX.
    9898
    99 Kristen: is the GLTF center-each-node option in the daily build? Elaine and Eric: after consulting daily build usage and code notes, yes, and true by default.
    100 
    101 Phil reports a problem with alphafold fetch, works for us in the same versions of ChimeraX, Eric figured out it was his connection to UniProt since it also doesn't work for him to use "open" on a uniprot sequence. Phil will report a bug. Followup: this was caused by his VPN since it went away when he turned it off. Ticket #16027
     99Kristen: is the GLTF center-each-node option in the daily build? Elaine and Eric: after consulting documentation, daily build usage and code notes, yes, and true by default.
     100
     101Phil reports a problem with alphafold fetch, works for us in the same versions of ChimeraX, Eric figured out it was his connection to !UniProt since it also doesn't work for him to use "open" on a uniprot sequence. Phil will report a bug. Followup: this was caused by his VPN since it went away when he turned it off. Ticket #16027
    102102
    103103At first we were confused that clicking "Fetch" on the !AlphaFold tool runs the command "alphafold match" instead of "alphafold fetch" but it makes sense upon reviewing the documentation: "alphafold match" accepts more ways of specifying the query, not just uniprot name/ID, and will get top hit from fast k-mer sequence search if no exact match.