[phenixbb] refinement at 3.7A

Christina Bourne bournecr at yahoo.com
Fri Apr 9 11:52:51 PDT 2010

Hi Vincent,
I can tell you from my work with a 5A virus capsid that NCS can make your maps look much better than the resolution dictates.  You didn't say how much NCS you have, but you may also consider NCS averaging as a tool.  Also be aware of high NCS contaminating the free set of reflections- I think Phenix can auto-magically pick in thin shells to mitigate this effect.

From: vincent Chaptal <vchaptal at mednet.ucla.edu>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Sent: Fri, April 9, 2010 12:35:15 PM
Subject: [phenixbb]   refinement at 3.7A

Hello list,

i would like to add a following discussion to yesterday's low resolution
refinement question: What is low res? at what resolution should we use
only rigid body refinement or can we use minimization as well?

In my case, i have a 2.7A and a 3.7A structures, of 2 different mutants,
in the same space groups and cell parameters. After refining the high
res one, i'm wondering what is the best strategy to refine the low res one?
If i do a simple rigid body refinement, I have R=32.1, Rfree=35.8. If i
use individual site refinement, i have R=30.7, Rfree=35.8. (both with
group ADP, TLS and NCS).
The statistics look good and the maps look great. There isn't any
feature in the difference map so i'm guessing i'm done with refinement?
(I'm afraid of over-refining it as the map look too good for this
resolution. )

I was also advised to add hydrogen bond restraints to maintain secondary
structures, I guess upon using minimization refinement?

Basically, could you update me on what's today's dogma on what type of
refinement we should use at what resolution?
( i couldn't find this info on the phenix web site, sorry if i missed it)
thank you very much.

Pavel Afonine wrote:
> Hi,
> rigid body refinement does not employ any restraints. You can use
> secondary structure restraints in refinement of individual coordinates.
> Actually, you can use secondary structure restraints in constrained
> rigid body refinement (SA in torsion angle space).
> To use secondary structure restraints:
> "secondary_structure_restraints=true". phenix.refine GUI should have
> an option for this too.
> Pavel.
> On 4/7/10 4:38 PM, r n wrote:
>> Hi
>> I wanted to do low resolution rigid body refinement with secondary
>> structural restrain. I have not seen
>> any command or information in the phenix document?
>> any help
>> Thanks
>> ram****
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Vincent Chaptal

Dept. of Physiology at UCLA


Phone: 1-310-206-1399

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