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 : [log in to unmask] >> 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! >