[phenixbb] phenix.refine v.1.3 vs 1.24

Pavel Afonine PAfonine at lbl.gov
Mon Oct 6 11:36:12 PDT 2008

Hi Leo,

I don't have the exact date, but I think it will appear sometime soon 
once I make this and a few other fixes.
If you run automatic weight optimization then it will skip that weight 
adjustment and it will try to find the best weight by optimizing the 
Rfree. Use "optimize_wxc=true" or/and "optimize_wxu=true" keywords for this.


On 10/6/2008 7:37 AM, Leo Sazanov wrote:
> 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?
> Regards,
> Leo
> 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!
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