Re: [ccp4bb] Refining residues as rigid bodies

x27;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

Re: [ccp4bb] Refining residues as rigid bodies

2 December, 2009 22:52:45 Subject: Re: [ccp4bb] Refining residues as rigid bodies 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 be

Re: [ccp4bb] Refining residues as rigid bodies

py 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 rat

Re: [ccp4bb] Refining residues as rigid bodies

K Sent: Wednesday, 2 December, 2009 8:56:01 Subject: Re: [ccp4bb] Refining residues as rigid bodies Dear Bulletin Board, I received this information from Axel Bruenger, who rightly corrected me on the modification to be made to the bindividual.inp file: >As an fyi, the sigmas should be made sm

Re: [ccp4bb] Refining residues as rigid bodies

Dear Bulletin Board, I received this information from Axel Bruenger, who rightly corrected me on the modification to be made to the bindividual.inp file: >As an fyi, the sigmas should be made smaller to get a narrower B-factor >differences. My previous post: > You modify the file bindividual.

Re: [ccp4bb] Refining residues as rigid bodies

3:51 > 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 h

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 par

Re: [ccp4bb] Refining residues as rigid bodies

Jason Porta wrote: I am currently refining a 3 ang structure and would like to do rigid body refinement treating each residue as a separate rigid body. Here's how you'd do it in Coot, but I'd be surprised if this was better that the "Fit Protein" function already built in (you'll need 0.6-

Re: [ccp4bb] Refining residues as rigid bodies

Hi Jason, yes, technically you can refine each residue as a rigid body in phenix.refine (as Fred explained), but: - why wouldn't you consider a more sensible (in my opinion) strategy running a combined refinement job that contains rigid body refinement of bigger rigid domains, SA in Cartesia

Re: [ccp4bb] Refining residues as rigid bodies

Hi Jason, Instead of doing rigid body refinement of each residue, you may consider rigid.inp of CNS or an equivalent strategy in Phenix which will do SA, rigid body and B factor refinement, followed by either composite omit (CNS) or 'prime & switch' of phenix (rather resolve) to "fix" the side cha

Re: [ccp4bb] Refining residues as rigid bodies

Hi, Looks as if you want to do rigid body refinement 'a la CORELS'. What about rigid body refinement in Phenix? From the Phenix manual: " If one have many rigid groups, a lot of typing in the command line may not be convenient, so creating a parameter file rigid_body_selections, containing the