help me to determine ligand's b fator?

From: 王瑞 <wangrui704

Dear Everybody,

    I am sorry for a little off-topic. Could anyone tell me how to determine a protein, peptide and ligand of a new pdb's b factor? I know there are rampage and sfcheck to validate in ccp4, but I only found a overall b factor in their result. By the way, are there a software to determine a new pdb's all parameters such as R_sym, I/σ, Redundancy, Solvent molecules' b factors?

Thanks

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From: Tim Gruene

Dear ,

A PDB file is a coordinate file. The quantities you mention, Rsym,
I/sigI, and Redundancy are quantities calculated from the measured data
and can therefore not be determined from a PDB file.

The PDB file also contains the B-factor, so in order to find out the
B-factors of some coordinates in the PDB file, you can open the file
with any text editor of your choice and look at its entries.

Best wishes,
Tim

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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From: Paul Emsley
You can use Coot to generate a new molecule for your residue selection
(or ligand) and then use the functions:

(average-temperature-factor imol)
(median-temperature-factor imol)
(standard-deviation-temperature-factor imol)

You can also use bfactan, which makes an xml file with temperature
factor statistics, IIRC.

Paul.

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From: Xiaopeng Hu
I made a simple script for this, perhaps you can edit it for your case.
Just save it as baverage.sh, then run it as  ./baverage.sh your.pdb.



#!/bin/bash
echo "----------------------------------"
grep '^ATOM' $1|cut -b61-66|cat |awk '{sum+=$1} END { print "     Protein Average B =",sum/NR;print "   Protein Atom Number =", NR}'
grep '^HETATM' $1|grep -v 'HOH'|cut -b61-66 |cat|awk '{sum+=$1} END {print "  Ligand/Ion Average B =",sum/NR;print "Ligand/Ion Atom Number =", NR}'
grep '^HETATM' $1|grep 'HOH'|cut -b61-66|cat |awk '{sum+=$1} END {print "       Water Average B =",sum/NR;print "          Water Number =", NR}'
echo "----------------------------------"


-


best,

xiaopeng

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From: Christian Roth
Hi,
as Tim pointed out Rsym, I/sigma, Redundancy could not be obtained from a pdb,
but you find it in the ouptut of SCALA, XSCALE, or similar scaling programs. I
use Moleman2 from the Uppsala Software Factory to get the B values out of my
pdb. F.e. "Bf St Type" provide B-Factors for every component in the file.

Christian

Am Mittwoch 12 Oktober 2011 13:53:56 schrieb 王瑞:

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From: Pavel Afonine
Hello,

Here is another option:

phenix.pdbtools model_statistics=true model.pdb 

or 

phenix.model_vs_data model.pdb data.hkl

which, among other statistics, will give you min/max/mean B-factor values for macromolecule, ligands, solvent.

Pavel 

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From: 王瑞 <wangrui704
Thank you for all your advice.They are all good suggestions!