[phenixbb] anisotropic refinement water hydrogens and gui

Christian Roth christian.roth at bbz.uni-leipzig.de
Tue Mar 9 08:58:19 PST 2010

Dear all,

I did an anisotropic refinement with the gui for a 1.6 Ang. structure I think 
this is quite O.K. as the R-values seems to be reasonable(14/18.8). But for 
comparison I want exclude waters and hydrogens explicitly from the anistropic 
refinement. One could do this in the command line mode via 
adp.individual.anisotropic ="not water and not element H. I started from the 
gui and modified the .eff directly by icnluding:
adp {
      individual {
        isotropic = None
        anisotropic = "not water and not element H"

In the output pdb all waters have an anisou flag. So I assume phenix refined 
them anisotropically. How do I have to modify the .eff file to exclude the 
waters from the anisotropic refinement. 
I would like to use the gui, because you get this nice summary output with all 

Phenix started optionally anisotropic refinement at 1.7 Ang. As far as I 
understand one should keep in mind that the data to parameter ration should 
have certain value of app. 3 or 4. But restraints as paramters are not as 
solid as experimental data. Is this 1.7 Ang. borderline a rule of thumb, is 
there a strict rule at which point I could refine anisotropic, or maybe mixed 
isotropic anisotropic. 

Best regards 

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