[phenixbb] low resolution refinement question

Pavel Afonine PAfonine at lbl.gov
Thu Oct 15 13:42:43 PDT 2009

Hi Peter,

here are a few considerations:

- ADP refinement: use TLS combined with group B-factor refinement (one 
isotropic B per residue).  It may be important to optimally define TLS 
groups. Use NCS.

- coordinates: You may need to use custom bonds to restrain secondary 
structure elements. Use NCS. Note, you can define the strength of each 
NCS group individually. Just in case the automatic weight are not 
optional, try put more weight on geometry by using "wxc_scale=...". Yes, 
conventional rigid body refinement with small rigid groups may be good 
at some point, but may be too brutal as well, so constrained rigid body 
refinement (torsion angle dynamics) may be a good option.

- mask: sometimes, using this "optimize_mask=true" makes a big 
difference at such resolutions, so you may want to try.

- rigid body refinement is completely disconnected from the NCS 
restraints (no any restraints used during rigid body refinement).


On 10/15/09 1:12 PM, Peter Grey wrote:
> Dear Phenix users,
> I refine a large complex  with three monomers in ASU at very low 
> resolution - 4.5A - and would like to ask two questions.
> - Could you give  some tips about refinement at this resolution other 
> than rigid body refinement - Can TLS and grouped B-factors work at 
> this poor resolution ?
> - I would really prefer that rigid body refinement will strictly obey 
> the NCS that was found in the molecular replacement solution. I 
> understand constrained NCS does not exist yet in phenix but is there 
> something approximate that can be used in rigid body refinement ? I 
> tried the conventional restrained NCS and the result was just like 
> without restrains.
> Thank you for your time ,
> Peter.
> ------------------------------------------------------------------------
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20091015/eeeef9ef/attachment-0003.htm>

More information about the phenixbb mailing list