Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

[ccp4bb] Summary torsion restraints in refmac
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2007 <-- October 2007 <-- 04 October 2007
Previous message:
Subject: Twinning: P43 apparently P42212
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2007-10-03 		Next message:
Subject: Open position at the Institute for Biochemistry (Advt. Nr. 07/B51)
From: Rajesh Kumar Singh singhrk {- at -} UNI-GREIFSWALD {- dot -} DE
Date: 2007-10-04


Subject: Summary torsion restraints in refmac
From: Eckhard Hofmann eckhard {- dot -} hofmann {- at -} BPH {- dot -} RUHR-UNI-BOCHUM {- dot -} DE
Date: 2007-10-04
Hi,
here a brief summary regarding the use of torsion restraints with i.e.
cofactors in refmac:

The current versions of refmac have two possible pitfalls if you refine
new cofactors and have a cif-dictionary including torsion angles and planes:

Torsions are NOT automatically used in refinement. You will notice this
if you switch on monitoring with 0sig for torsions, which should show
you all torsions used in refinement. To use torsion restraints you have
to include a line like this in the input:

restr tors include resi XXX name var_1 value 180.000 sigma 5.000
period 2

This manually adds one torsion definition to the refinement. Note, that
this torsion has to be defined in the cif-dictionary (which atoms belong
to it), but the actual values are now taken from the input line! The
values in the cif are not used.
CCP4i-User: You have to use the "Developers Options" to include a
keyword file with the above lines! Otherwise your torsion will never be
used!
The second possible pitfall is, that currently the sigmas assigned for
plane definitions in the cif-dictionary are NOT used, but instead
general default values are used.


Garib was so kind as to tackle the torsion definition immediately.
There is an experimental version at

www.ysbl.york.ac.uk/refmac/data/refmac5.4_linintel.tar.gz

Now you can use the following line to include all torsions of a specific
residue:

restr tors include resi XXX

or to include only one specific definition in refinement

restr tors include resi XXX name var_1

Note that the torsion definitions have to start with "var" !
Values and sigmas will be taken from the cif-dictionary.
You can override single values explicitly by stating a full line with
new values.

The issue with the sigmas for plane definitions will be dealt with soon
by Garib.

Eckhard



--
Eckhard Hofmann
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762
ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd