[phenixbb] Weird Hydorgen refinement

Pavel Afonine pafonine at lbl.gov
Mon Aug 22 17:55:20 PDT 2011

Hi Yuri,

there must be an error somewhere: in the program or in your parameter 
files. Did you run phenix.refine from GUI or command line? Can you send 
me the *eff and *log files?

If you used GUI what exactly you clicked?

What is the version of PHENIX?

What's in input PDB: does it contain any ANISOU records?


On 8/22/11 5:44 PM, Yuri wrote:
> Hello everyone.
> I was trying to refine my model anisotropically. I selected element NA 
> or (chain A and not element H).
> I looked at the output pdb shows that hydrogens were being refined 
> anisou as well as the protein.
> I believe its because technically they are also in chain A, but 
> shouldnt the default be never refine H's anisotropically, especially 
> at 1.5A ?.

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