We faced a similar situation recently where our molecular replacement suggested 2 molecules in the asymmetric unit but the B factors of the second chain were twice as large as the first protien chain. At a resolution of 1.8 Å2 you could see the electron density for both chains. We performed ARP/wARP and realized only part of this second chain is resolved in our structure. It was model bias.
Best, Engi Engi Hassaan PhD Student Research Group of Prof. Dr. G. Klebe Marburg, Germany On Mon, Jul 22, 2019, 19:34 Bernhard Rupp <hofkristall...@gmail.com> wrote: > > Could there be two versions of each model: a "robustly-observed" and a > "most-likely" version? > > We tried/suggested something in this spirit once. Not sure how it was > received.... > http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html > > Best, BR > +++++++++++++++++++++++++++++++++++++++++++++++++ > 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=rOm2j6iwxpg727UzObri1TbWnpwIi > ZjKQvFr6ZVB9DY&s=Fk1bBPINkOI2P2wVJmv4cG2X8T6P0PwFqvAiyyTVnBk&e= > <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 > > ######################################################################## > > 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
