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 Date: 2024-01-05 23:48 To: CCP4BB 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¶ baverage XYZIN foo_in.pdb RMSTAB foo_out1.tab XYZOUT foo_out2.pdb [Keyworded input] 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 <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, a mailing list hosted by 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 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/
