As Robbie says, in such a case I just blindly refine with local NCS restraints - this should improve the greater part of the model and thus provide you with clearer maps. It is quite common for different copies of the monomer to have differences - after all the crystal environment will be different - but this should become clearer as refinement progresses. The programs are pretty good at smudging out errors - B values usually go sky high, and once you have a better map you can set the occupancies of the poorly ordered bits to0.00 and see what, if anything comes back. Eleanor
On Wed, 12 Apr 2023 at 10:27, Robbie Joosten <[email protected]> wrote: > 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 <[email protected]> On Behalf Of Nitin > > Kulhar > > Sent: Wednesday, April 12, 2023 10:02 > > To: [email protected] > > 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/ > ######################################################################## 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/
