Well - I turn off occupancy refinement once there is a sort of consensus.. Disulphides often break after long exposures and you see the positive and negative blobs clearly. I must admit I usually just set 0.5 as occ , fix the surviving disulphide link and let the B values suggest a better ratio than o.5:0.5.. Eleanor
On Mon, 6 May 2024 at 20:20, Liliana Margent <lmarg...@gradcenter.cuny.edu> wrote: > Greetings everyone, > > I'm currently in the process of modeling a disulfide bond in two > structures. However, when I attempt to model single occupancy for the > cysteines involved in the bond, negative density blobs emerge within the > disulfide bond. This suggests the possibility of alternate conformations > for the cysteines. > > Yet, when I endeavor to model alternate conformations for both cysteines, > their occupancies do not align despite running refinement with a bond > parameter file that specifies the link. To illustrate, I initiate the > refinement with occupancies for Cys472 as A0.75/B0.25 and for C384 as > A0.75/B0.25, but post-refinement, the output occupancies appear as Cys472 > A0.84/B0.16 and for C384 A0.97/B0.03. Where A confs participate in the s-s > bond. > > Has anyone else encountered this issue before, or does anyone have > suggestions on how to refine these cysteines to achieve coherent > occupancies? > > Thank you for any insights you can provide. > > Best, > Liliana > > ######################################################################## > > 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/
