Hi Engi, I understand that you say that the 2nd molecule in your case is not real; it's just model bias?
I would not come to this conclusion. B values of NCS-related chains being quite different is not that rare. In my experience, at 1.8A and with a reasonably refined model (Rfree less than 30%), continuous electron density (even if it is visualized at low sigma) matching the model does not arise from model bias,. From your description, I infer that the second molecule exists in your crystal; it's "just" poorly ordered (or at least worse than the first) - otherwise ARP/wARP wouldn't build part of it. That ARP/wARP does not build the rest does not mean that a human cannot or should not build it, nor that it should not be built; the automatic programs typically only build the good parts. The statistics of the MR solution should tell whether the 2nd molecule was found due to a significant signal (LLG increase in phaser; good contrast in molrep), or because the user was "asking" the program to position two molecules. What is R/Rfree with/without the 2nd molecule? (Peer says that in his case the difference is 0.3% which I'd say is an insignificant difference) Can the crystal lattice be continued in all 3 dimensions without the 2nd molecule? best, Kay On Tue, 23 Jul 2019 06:22:31 +0200, Engi Hassaan <[email protected]> wrote: >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 <[email protected]> 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 <[email protected]> On Behalf Of Peer Mittl >> Sent: Monday, July 22, 2019 6:05 AM >> To: [email protected] >> 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
