IHM-repval February 2017

ihm-repval@salilab.org

3 participants
2 discussions

Linking integrative models out to experimental data
by Ben Webb 13 Mar '17

13 Mar '17

Hi all, As you know, whenever we build an integrative or hybrid model we need to point to multiple sources of input experimental data. It doesn't make sense to embed that data directly in an mmCIF file because that would be very inefficient, so instead we need to link out to wherever the raw and/or processed experimental datasets are stored, ideally in a repository maintained by experts in the field (e.g. PDB, EMDB, SASBDB). I've summarized the kinds of data that we've been dealing with so far in our own modeling, with pointers to repositories where available, in the wiki: https://github.com/ihmwg/IHM-dictionary/wiki/External%20data Please take a look and add to it (or reply to this email). It seems likely that there are many modeling scenarios that neither RCSB nor the Sali lab have considered thus far. Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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wwPDB representation / validation group
by Andrej Sali 23 Feb '17

23 Feb '17

Hi all, As you know we meet weekly over Skype to discuss issues related to the representation and validation of integrative models: https://github.com/ihmwg/IHM-dictionary/wiki/Meetings <https://github.com/ihmwg/IHM-dictionary/wiki/Meetings> These meetings tend to focus on technical details related to the mmCIF dictionary. However, we're starting to have monthly meetings where we have a more high level discussion among a larger group of people. If you can only make an occasional meeting, we recommend these are the meetings you come to. The next such large-group meeting will be on February 23rd, 2017 at 9am Pacific time (noon Eastern). If you're interested in attending, please let Brinda Vallat at RCSB know, so she can add you to the Skype call: brinda.vallat(a)rcsb.org <mailto:brinda.vallat@rcsb.org> If this time is really inconvenient for you, please let Brinda know and we can look into other times. Best, Andrej -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org _______________________________________________ IHM-repval mailing list IHM-repval(a)salilab.org https://salilab.org/mailman/listinfo/ihm-repval

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IHM-repval February 2017