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!