[phenixbb] refinement in low resolution

r n ramme29 at yahoo.com
Tue Dec 15 15:20:39 PST 2009

thanks Pavel.

I did tight the restrain and R/Rfree drops to 37/41 % with rms for the monomer is around 0.12.

Also I did surprise to see the ranges of R factor while doing simulated annealing but final R-factor 
goes high to 37/41 % ? 

Is it anything wrong with convergence?
   step=   50 temperature= 2284.4 rmsd=0.6256 r_work=0.3061 r_free=0.3564
   step=   75 temperature= 2174.4 rmsd=0.7957 r_work=0.2978 r_free=0.3483
   step=  100 temperature= 2064.4 rmsd=0.8910 r_work=0.2978 r_free=0.3681
   step=  125 temperature= 1954.4 rmsd=0.9354 r_work=0.2977 r_free=0.3710
   step=  150 temperature= 1844.4 rmsd=0.9684 r_work=0.2953 r_free=0.3793
   step=  175 temperature= 1734.4 rmsd=0.9924 r_work=0.2928 r_free=0.3819

Is it possible to ncs averaging , especially multi-domain averaging in heterodimer molecule using phenix.


From: Pavel Afonine <PAfonine at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Sent: Tue, December 15, 2009 11:14:51 AM
Subject: Re: [phenixbb] refinement in low resolution

I am trying to refine the model in low resolution and there are
>multimer in the asu.
>>I did rigid body refinement after MR , molecule did not move much and
>R/Rfree stays 45 % 
Did you define multiple rigid groups for rigid body refinement? If not,
then it's not too surprising that it didn't move much since the MR
programs typically do a good job on rigid body refinement anyway.

So, use "sites.rigid_body" keyword for this.

If I do simulated annealing or any type of refinement
>(group_adp), Rfree is high and R goes down, but
>>the if do the superposition of the monomer, rms is 1.5 to 1.8. 
Try SA in torsion angle space (main.simulated_annealing_torsion=true).
At this resolution you may need to refine one ADP per group (say per
residues or any bigger selected group of atoms). Also, use TLS. Use NCS
if available, and you can defined it's strictness by adjusting
appropriate weights.


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