Joe

I guess you are correct.  I'll have a closer look.

Nigel

On 9/28/09 4:18 PM, Joe Krahn wrote:
GeoStd seems not to have an files. Is it only available via SVN for now?

The GeoStd parameters still need some work. The equivalent hydroxyls are 
not symmetric. One of the dihedrals has a base angle of -175.0 instead 
of 180 (or +/-60). One has an esd of 30.0, and the others have an esd of 
20.0. The hydrogen ESDs also seem a bit too tight, and probably should 
have a periodicity of 3.

They are an improvement, but I don't think automated parameterization 
will ever be perfect.

Joe

Nigel W Moriarty wrote:
  
Joe

It is in the nightly builds if you are inclined.  You are also free to 
download the restraints from the GeoStd open source project.

Nigel

On 9/28/09 1:43 PM, Joe Krahn wrote:
    
Nigel,
I am using PHENIX 1.4-6, which is newer that the most recent version on 
the PHENIX web site, other than "nightly build" versions.

Nigel W Moriarty wrote:
  
      
Joe

I think you may need to upgrade your version of PHENIX.  In the current 
version, the periodicity is 3.  I have recently been using eLBOW, the 
Chemical Components library and the Monomer Library to improve any 
residue restraints that have short comings.  These are freely available 
at Source Forge from a project called GeoStd at 
http://sourceforge.net/projects/geostd

Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd

Nigel

On 9/28/09 11:45 AM, Joe Krahn wrote:
    
        
I found that residue TRS has different dihedral target angles for the 
three hydroxyl oxygens, which are actually all equivalent. They have a 
periodicity of 1, but should have a periodicity of 3. What is the best 
way to handle such discrepancies?

Most ligand parameters are probably auto-generated based on a reference 
structure, and there is probably a lot of conformation bias. In this 
case, it seems that parameterization should have been able to detect 
symmetry. It would be nice if parameters could include information about 
whether a human has done any validation. Actually, a ligand Wiki might 
be nice, where people can easily put comments, even if they are not sure 
about how to improve the parameters.

Joe Krahn
          
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
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