Dear community, I would like to know the community opinion in a topicregarding the deposition of Pandda events maps as part of SF factors of thehits on deposition.
In a recent deposition, I was required by PDB to add to my SFfile a block containing ‘data for ligand evidence map’, aka Pandda event map,as this would be crucial for people to ‘reproduce my results’. I found out in the hard way that converting .ccp4 to a .mtzis not a trivial task, as the first lack many crucial crystallographic information(such as symmetry and I/sig). Eventually, I found a way to do it (thanksTobias), by expanding original symmetry to P1, realign origin of the map and convertingwith phenix.map_to_structure_factors, which is quite a lot of work if you havemany hits. I’m sure this people in this BB would have better ways to do it (Iwill be happy to hear them), but this is not the goal of this post. The goal is to bring to discussion the relevance of havingthe event map block added to the SF files in PDB. As I understand, this astatistical map calculated from averages of several datasets from your eventsearch, with the only goal of highlighting weak signals. The way I see it, thereis no crystallographic information at an event map that can be anyhow used forvalidation a structure (at least with our standard tools). Moreover, as this mapis calculated from a large set of datasets (mostly apo structures notdeposited), there is no way anyone would reproduce a given map without having accessto all the used files from pandda input (mostly apo structures that are not deposited). On the other hand, there is of course the fact thatsometimes week events are hard to be proved only by the SF, and visualizationof the event map is keen for its confirmation. So, my question is, is it worth it to having this informationattached to the SF files of the deposited ligand-bound structures? Maybe thereis a better way to do it. I though maybe if PDB allowed us to upload event mapsas ‘auxiliary files’, same way they do with cryoEM files (like masks, modifiedmaps, etc), so we can have our visual confirmation of the events if we wish,and at the same time not polluting our xray files with information that is notxray. I will be glad to hear about that from the communitie, Thank you so much Andre S. Godoy, PhD Universidade de São Paulo Instituto de Física de São Carlos Av. João Dagnone, 1100, Jd. Santa Angelina13563-120 - São Carlos, SP, Brazil ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
