Hi Sorbhi, The Geman-McClure weight (alpha) controls robustness to outliers. As this value is raised, more restraints are treated as outliers and down-weighted. This will allow local conformational differences where there are dissimilarities between target and reference structures.
So if you really really want the restraints to be used (e.g. if you're trying to force something to be more helical) then you can use a lower alpha. Though if there may be some real differences between the restraints and the true structure - e.g. if you're using restraints based on a homologue - then you might want to use as slightly higher alpha so that regions displaying larger discrepancies from the restraint targets will not be influenced by the restraints. If you're using self-restraints then it's a balancing act - you want the structure to be stabilised, but you also want to allow it to deform enough to allow local structure to find the correct place in the map. In Refmac values around 0.01-0.02 are typical. In Coot it varies - potential use cases during model building can be more varied than in refinement. The overall strength of the restraint weights also plays a big part, so it's a case of trial and error. Maybe Paul can advise about his preferred strategy? Fortunately in Coot it's easy to try different values, and the real time visual feedback of refinement performance should make it intuitive to see whether the alpha should be increased or decreased, especially when looking at more difficult regions. Paul's got some videos of this in action, e.g.: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/movies/refine-example-nov.ogv Regards, Rob > On 12 Oct 2020, at 13:44, Sorbhi Rathore <[email protected]> wrote: > > Dear all, > > Could anyone please suggest the best way to decide which German- McClure > Alpha value to use during refinement (both at a higher resolution and lower > resolution areas for a cryo-EM map)? > I am using coot 0.9.1 pre EL(ccpem). > > Best wishes, > Sorbhi > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
