Dear Trevor, I do not know if you are aware of it but there is a different version of refmac which is just made for Cryo-EM refinements. (http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/software.html)
In there, Refmac reports an average FSC value which is way more useful than the R-factor. You want to have this value as high as possible (based on your resolution it might be around 0.79) But you always have to make sure to not do overfitting. You will have to test for overfitting as it is described and done for example in the most recent publications of Venki Ramakrishnan. Cheers Marcus Marcus Fislage, PhD Howard Hughes Medical Institute (HHMI) Columbia University Department of Biochemistry and Biophysics Lab of Joachim Frank New York, NY email address: mf2...@cumc.columbia.edu Phone: 212.305.9524 Fax: 212.305.9500 Marcus Fislage, PhD Howard Hughes Medical Institute (HHMI) Columbia University Department of Biochemistry and Biophysics Lab of Joachim Frank New York, NY email address: mf2...@cumc.columbia.edu Phone: 212.305.9524 Fax: 212.305.9500 ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Trevor Sewell [trevor.sew...@uct.ac.za] Sent: Wednesday, February 01, 2017 12:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac5 and Coot for refining cryo-EM structures I have a 3.4 A (enzyme – protein only) map that I have fitted manually using Coot and automatically with Rapper. It all looks very nice – I can fit all but 13 of the 330 residues. I have the following questions: Does refmac5 have a way of refining the scale of the map? – I did my best to calibrate the microscope – but it would be nice to have the scale as a refinable parameter. Is there a way of having Coot know that it is an electron map and not an x-ray map? The main issue is that carboxyls seem to be invisible and Coot tries to fit them as though the map had them there – which results in some pretty dopey stuff. The problem doesn’t seem to apply in refmac5 if you use the source EM as described in the instructions. What is a reasonable starting weight for vdwrestraints ? Is there a rule of thumb for choosing this? What are acceptable values for the Rfactor produced by Refmac5? The fit looks pretty good with an Rfactor of .39. What is the experience of the community in this regard? Many thanks Trevor Sewell Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via cs...@uct.ac.za
