Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Sat, 06 Jan 2024 01:13:25 -0800


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
 
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

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








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