This is the old question of what a structural model represents. One perspective is that it represents the things one is certain about above some threshold, from the crystallographic data and maps alone. The other perspective is that it represents the most likely guess of what is actually there. I prefer the second "most likely" approach since it incorporates more information, namely the knowledge of what's in the solutions, the way proteins pack, the protein's sequence, etc. And everyone agrees to the use of such priors when it comes to bond lengths and similar. I guess it boils down to the weighting of prior information.
A problem arises, however, when users from one camp look at models from the other camp, and I do not really have a solution to this, especially as the two camps don't tend to see both sides of the question. Could there be two versions of each model: a "robustly-observed" and a "most-likely" version? Maybe this debate could also be raised at the Holton conference? Jacob +++++++++++++++++++++++++++++++++++++++++++++++++ Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 +++++++++++++++++++++++++++++++++++++++++++++++++ The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Peer Mittl Sent: Monday, July 22, 2019 6:05 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Density questionable? Dear Colleagues, We are working on a structure where the density for a whole protein chain (>200 aa) is questionable, since the B-factors exceed 200 Å2 (2.3 Ang resolution). However, the initial difference density map and the feature enhanced map (normal 2fo-fc map to a minor extend) support the presence of this chain. Putting the chain seems equally wrong as not putting it. Putting it reduces Rfree by 0.3%. As a conservative researcher I feel tempted to deposit the structure without this highly mobile/weakly occupied chain, but other researchers may say "he has missed something". Handling this chain like a weakly occupied water is probably wrong, but what is the optimal/correct way? Is there a general opinion on how the escape this dilemma? All the best, Peer ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwID-g&c=LU6cRtx0xgB8s29tIz9Olw&r=eLCg9eJ4Rs_LnxfUWsp7FSxhIEcZYmTSU4Uyq1bRYPI&m=rOm2j6iwxpg727UzObri1TbWnpwIiZjKQvFr6ZVB9DY&s=Fk1bBPINkOI2P2wVJmv4cG2X8T6P0PwFqvAiyyTVnBk&e= ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
