[phenixbb] anisotropic refinement water hydrogens and gui
christian.roth at bbz.uni-leipzig.de
Tue Mar 9 08:58:19 PST 2010
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:
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
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