Isnt it most likely that this chain is partially occupied? Eleanor
On Mon, 22 Jul 2019 at 12:32, <[email protected]> wrote: > 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:[email protected]] Im Auftrag von > Peer Mittl > Gesendet: Montag, 22. Juli 2019 12:05 > An: [email protected] > Betreff: [EXTERNAL] [ccp4bb] Density questionable? > > EXTERNAL : Real sender is [email protected] > > > > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
