It appears that Zhonghao might be worried about his data to parameter ratio. At 3 A, one can easily be in a situation where one has fewer reflections than four times the number of atoms (X, Y, Z plus B). I like the idea of starting out with the average B (or even Wilson B) and then doing TLS as that should reduce the number of parameters being refined. Best regards, tom
________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Robbie Joosten <robbie_joos...@hotmail.com> Sent: Saturday, January 6, 2024 8:13 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group? You don't often get email from robbie_joos...@hotmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> One wonders who those "many people" are. You may not want to use them as your go-to reference for refinement techniques. Anyway, Refmac cannot do grouped B-factor refinement, but you are not missing out on anything. As Eleanor implied, one-per-residue B-factors give unrealistic results. You are much better off using isotropic B-factors with tight restraints (Refmac's default is already quite tight). Add TLS in your refinement to see if that helps. If you have a really poor data/parameter ratio you could go for a flat B-factor model and try to capture most of the B-factor in the TLS model. This is typically not needed at 3A, but there are exceptions (low solvent -more atoms- or low completeness -fewer reflections- are factors to consider). If you do go for a flat B-factor model, you need to define sensible TLS groups. This takes some trial and error. pdb-redo has decent algorithms to select the B-factor model and weight for Refmac. You could use that as a starting point for your model. HTH, Robbie On 6 Jan 2024 03:13, "chenzhonghao...@163.com" <chenzhonghao...@163.com> wrote: Dear Prof. Dr. Dodson and all CCP4 community, Thanks for your reply. Just now, I used baverage. I found that it can average the B factor but not refine it. This function does not fit my requirement, because my resolution is low as 3 A. Many people said that Refmac5 overrefines the structure if I used isotropic temperature refinement. Did refmac5 or other programs in CCP4 have similar functions like one_adp_group_per_residue or two_adp_groups_per_residue in Phenix? Any help would be highly appreciated! ________________________________ chenzhonghao...@163.com From: Eleanor Dodson<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Date: 2024-01-05 23:48 To: CCP4BB<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group? Hmmm - I am not sure about the value of this - one expects the longer floppier side chains to have very different B values for the CB than the OE2.. The program BAVERAGE gives you a plot of mean B value residue by residue.. baverage - averages B over main and side chain atoms SYNOPSIS¶<https://www.ccp4.ac.uk/html/baverage.html#synopsis> baverage XYZIN foo_in.pdb RMSTAB foo_out1.tab XYZOUT foo_out2.pdb [Keyworded input<https://www.ccp4.ac.uk/html/baverage.html#keywords>] DESCRIPTION¶<https://www.ccp4.ac.uk/html/baverage.html#description> A very simple minded program to read a PDB file, tabulate to RMSTAB the average B values residue by residue (main chain and side chain separately) and the RMS deviation of the B values from this mean. It also outputs a PDB file with outlying B factors reset to lie within the given range. On Fri, 5 Jan 2024 at 03:08, chenzhonghao...@163.com<mailto:chenzhonghao...@163.com> <chenzhonghao...@163.com<mailto:chenzhonghao...@163.com>> wrote: Dear CCP4 community, I found that Refmac5 refined the temperature factor only by four modes (see the bottom of the attached figure). However, no grouped B-factor (one or two per residue instead of one per atom) was found. Actually, PHENIX and CNS can do it. But we are not familiar with both software. I want to know whether Refmac5 refines one or two group B per residue (for side and main chains) grouped temperature factor? Any help would be highly appreciated Thanks in advance. best, Zhonghao Chen ######################################################################## 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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
