The fact that your protomers have different density levels does not mean they are structurally different. The prior assumption should be that they are the same unless proven otherwise. So I would keep the (local!) NCS restraints in the initial stages and only remove them if it becomes apparent that this hurts refinement. No need to worry about the density averaging out. The models may average out but the density should still have enough signal to show any real differences.
HTH, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Nitin > Kulhar > Sent: Wednesday, April 12, 2023 10:02 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] NCS consideration during refinement vis-a-vis ligand > occupancy and flexible loops > > Hello all > > I am writing to request opinions from the community regarding the following: > > Situation: An ASU comprising a non-crystallographic homo-octamer of a > biological monomer was obtained from MR. Electron density in the initial 2Fo- > Fc, as well as Fo-Fc maps, seems to vary widely* across the eight protomers > for > > * the supposedly co-crystallized ligand (Kd ~100 micro-molar, determined > with ITC) and > * 1-2 flexible loops (too far from the ligand to interact with it > directly) > > > Decision: Before commencing to do refinement in such a case, would it be > advisable to omit the flexible loops / binding site residues from the NCS > reference group to avoid inadvertently averaging out the density of structural > elements with partial occupancies (ligands and flexible loops)? > > * varying from non-existent in some protomers to huge unmodeled blobs in > others. > > Please write for any clarifications / further details. I would be highly > grateful for > any help in this regard. > > Best regards. > > Nitin Kulhar > > PhD student > c/o Dr Rajakumara Eerappa > Macromolecular Structural Biology Group > Indian Institute of Technology Hyderabad > Kandi, Sangareddy > Telangana, India - 502285 > > Disclaimer:- This footer text is to convey that this email is sent by one of > the > users of IITH. So, do not mark it as SPAM. > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
