Thank you so much From: Eleanor Dodson <eleanor.dod...@york.ac.uk> Date: Monday, May 6, 2024 at 3:30 PM To: Liliana Margent <lmarg...@gradcenter.cuny.edu> Cc: CCP4BB@jiscmail.ac.uk <CCP4BB@jiscmail.ac.uk> Subject: [EXTERNAL]Re: [ccp4bb] Modeling Disulfide Bond Occupancies ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.***
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<mailto: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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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/
