[phenixbb] phenix.refine v.1.3 vs 1.24

Leo Sazanov sazanov at mrc-dunn.cam.ac.uk
Mon Oct 6 07:37:37 PDT 2008

Hi Pavel,
Thanks for suggestions. I tried riding hydrogens and weight 
optimizations - they didn't change things significantly.
I'll wait for version without automatic weight adjustments to see if the 
reason for difference between the versions might become clearer.
Are there any plans for when it might be released?

Pavel Afonine wrote:
> Hi Leo,
> I can't tell what exactly happens in your case. Below are a few points...
> - Version 1.24 is very old and we fixed lots of problems and made many 
> improvements / features since that time. So, I would suggest to use 
> version 1.3 anyway.
> - I will add an option so one can turn the automatic weights 
> adjustment off.
> - I haven't done any systematic investigation but I've seen some cases 
> where ml target produced "better" results than mlhl (unexpected) and 
> inversely (as expected).
> - Did you try to use riding hydrogens? In many cases this improves the 
> model geometry.
> - You may also want to run an automatic weight optimization procedure. 
> Please note it may take a while to run (depending on model size and 
> data resolution).
> Cheers,
> Pavel.
> On 10/3/2008 9:18 AM, Leo Sazanov wrote:
>> When refining the same (large) molecule in several different crystal 
>> forms at about 3.1 A resolution, I noticed that in two cases when 
>> experimental phase information is available, in phenix.refine-1.3 I 
>> get worse Ramachandran compared to phenix.refine-1.24 - about 2% less 
>> residues in most favored regions. In one case when there is no 
>> experimental phase information, there is no difference between two 
>> phenix versions.
>> What could be the reason for that?
>> These comparisons where done for cases when final RMSDs and R-factors 
>> are similar (and all RMSDs calculated in v.1.3), so automatic weights 
>> adjustment in v.1.3 should not have played much role. Adding to other 
>> people's comments, it would be useful to be able to switch this 
>> adjustment off, as sometimes one wants full control over final RMSDs, 
>> etc.
>> Thanks!

Dr. Leonid A. Sazanov
Research group leader
Medical Research Council
Dunn Human Nutrition Unit
Wellcome Trust / MRC Building
Hills Road
WEB: www.mrc-dunn.cam.ac.uk
Tel: +44-1223-252910
Fax: +44-1223-252915

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