Dear Peer, I did not check, but I expect that atoms with B-factors exceeding 200 Å2 will not contribute much to the F's at 2.3 Å. A good test might be to calculate Rfree's at 4 or 4.5 Å (no refinement!) to see if the missing protein chain contributes at low resolution. If it does, I would keep the model, if it doesn't, you can consider removing the model.
My 2 cts, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Peer Mittl Gesendet: Montag, 22. Juli 2019 12:05 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Density questionable? EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 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=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=O7j1uat8N4jZ5bcK8ivZZRoqkd5rA-z7mp1aFu1o5_I&s=zNdgTjxGzkcfsoQMY49XR7dq0MCRlmBUJxcD_vWG-y4&e= ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
