Hello Derek,
You might receive more answers if you post cryoEM questions to the CCPEM list: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=ccpem Not sure why you need to refine a B-factor, at this resolution it won't tell you much, even with only one per chain or per tetramer. For the rigid-body fit, I suggest following one of the approaches I mentioned in this other discussion: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;f355f637.2411 You can subsequently run phenix.real_space_refine with coordinate refinement turned off and B-factor refinement turned on: you will get one B-factor per atom, but then you could take the chain- or tetramer-average as your final value? Regarding which map to refine against: phenix and servalcat both accept or even require half-maps as input, so you mostly don't get to choose. Half-maps are always assumed to be un-filtered/un-sharpened (which is how they are when taken fresh out of your cryoEM 3D refinement job, at least in RELION and CryoSPARC). Whether using a sharpened map is justified for coordinate refinement (if your model refinement program of choice accepts a single map) is worth asking and discussing. But for B-factor refinement you need the "raw" map, because with enough sharpening you could drive atomic B-factors to any arbitrarily low value, and in this case they would no longer describe the experimental uncertainty (and I don't know what else one would need atomic B-factors for). I hope this helps, Guillaume ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Derek Logan <0000ac2332bb2871-dmarc-requ...@jiscmail.ac.uk> Sent: Monday, December 16, 2024 3:39:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Cryo-EM rigid body with 1 ADP per chain Hi everyone, I would like to do a quick rigid-body refinement of a model against a low resolution (6 Å) cryo-EM map. The model consists of four tetramers and I want to refine each tetramer as a rigid body, either with one (anisotropic?) ADP per tetramer or at the most one per chain. I haven't yet found a good way to do this. With phenix.refine the default is one ADP per residue and I can't see how to change that behaviour (at least through the Phenix GUI). I tried Servalcat but I can't see a way to restrict it to rigid body only. Given more time, I hope to reach a fuller understanding of each program, but I need to solve the immediate problem in the next couple of days (what with Christmas coming up...) Any suggestions? I have also understood that the best practice is to refine against the unsharpened map, correct? Thanks Derek _____________________________________________________ Derek Logan Professor | Biochemistry and Structural Biology Centre for Molecular Protein Science Lund University, Box 124, 221 00 Lund, Sweden www.cmps.lu.se ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## 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/
