Hi Harry, Yes, this is easy to answer! There are various papers, some from my group, about the utility of AlphaFold models in MR. For the specific point of how to treat the models, you can look at the paper on process_predicted_model (https://doi.org/10.1107/s2059798322010026), which is available in both Phenix and CCP4. In CCP4, there’s also the SliceNDice tool.
The side chains are considerably better than random, so they’re left in for any residues included in the model. But yes, it’s good to prune out low confidence residues, with 70 being the most common cutoff. The trickiest bit is deciding where there might be inter-domain flexibility. Domain parsing can be done in a variety of ways in process_predicted_model and SliceNDice, but the human eye is also very good at the required pattern recognition! There’s something I like to reiterate whenever possible, because we keep seeing people making this mistake. Whatever you do, don’t use the model straight out of AlphaFold! These have the pLDDT in the B-factor column, on a scale of 0-100 where 100 is nearly perfect. If you leave them as B-factors, you will be down weighting the very best parts of the model in the MR calculation! If you process the model, the pLDDT values will be turned into B-factors that are low for high pLDDT and vice versa. Best wishes, Randy From: CCP4 bulletin board <[email protected]> on behalf of Harry Powell <[email protected]> Date: Saturday, 24 January 2026 at 15:56 To: [email protected] <[email protected]> Subject: [ccp4bb] pruning & confidence of AlphaFold models for MR Hi folks I’m sure that people have thought about this, done this, and maybe even published on the topic, so this should be an easy one to answer :-) I was wondering how people treat AlphaFold models when using them in molecular replacement? Do they prune them down to poly Ala, do they include all modelled residues or remove those with low confidence (if so, how low - pLDDT 70?)? Harry ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C9a680370d247425d6af508de5b613213%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C639048670160264599%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=xIPgNoHXqqATin9xL2qJ6fSY8gDD95VTXvbP0vPdklQ%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C9a680370d247425d6af508de5b613213%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C639048670160291709%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=FyxnNuZ1K1o%2Fy72%2BmxzcAIep3sw4WLzjhEqL56TZuy8%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C9a680370d247425d6af508de5b613213%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C639048670160311594%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Zzj5poOnPPApciMB2vfp2S%2FZndQ3cfPCLIPrvFb4lV8%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C9a680370d247425d6af508de5b613213%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C639048670160330083%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=g4co4EmBAaJXe0JvtVfD0DSy5XDBYF7KEr1sv26ibgg%3D&reserved=0<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/
