Hi,
you can do similar thing (that is resulting in similar outcome) in
phenix.refine by increasing the weight on ADP restraints term. Example:
increase "wu" or decrease "wxu_scale". Although I believe a regular
refinement of individual isotropic ADPs should normally work just fine
at 3A resolution in phenix.refine.
Pavel.
On 12/1/09 11:18 PM, Frederic VELLIEUX wrote:
If the problem is B-factor refinement, you can do that easily at low resolution
with CNS. You just give tight restraints.
You modify the file bindividual.inp
This section:
{* target sigma values for restrained B-factor refinement *}
{* mainchain bonds *}
{===>} bsig_main=1.5;
{* mainchain angles *}
{===>} asig_main=2.0;
{* sidechain bonds *}
{===>} bsig_side=2.0;
{* sidechain angles *}
{===>} asig_side=2.5;
I cannot remember in which direction the values have to go. I think up. I have
done this with a very low resolution structures (4.5 A?) a few years ago, you
get smoothly varying B values, very tightly restrained. I do not think we
published that structure, we obtained a higher resolution structure later (I
don't think the referees would have been very happy seeing B factor refinement
at low resolution). But it worked.
Fred.
Message du 01/12/09 23:51
De : "Jason C Porta"
A : CCP4BB@JISCMAIL.AC.UK
Copie à :
Objet : Re: [ccp4bb] Refining residues as rigid bodies
Basically my reasoning for doing this is a low data-to-parameter ratio, which
makes B-factor refinement unfeasible. So far I have had nice results with
breaking the complex into rigid subdomains. So i was basically just thinking of
a way I could refine the structure best, without using too many parameters.
I see now how this can be done in Phenix. I will give it a try.
Thanks for all of your suggestions!
