[phenixbb] riding hydrogen and mlhl

Paul Adams PDAdams at lbl.gov
Tue Mar 27 12:19:22 PDT 2007

Hi Jianghai,

   if you obtain the latest CCI Apps you will see that there is a new 
program, phenix.reduce. This is the reduce program from the Richardsons 
Lab at Duke. This is very experimental at the moment, but I believe you 
should be able to add hydrogens to your structure using phenix.reduce 
and then read that into phenix.refine. I know that Pavel has only 
started work on this recently so I can't promise it will work as 
expected, but he has run some initial tests that look promising (1-2% 
drop in R-free after adding hydrogens).


Jianghai Zhu wrote:

> Hi All,
> I just found a refinement.hydrogens entry in the phenix.refine.  Can we 
> use phenix.refine to generate riding hydrogens to help the geometry in 
> low- or mid-resolution refinement now?  Using hydrogens in refmac5 
> really gives a better result than not using hydrogens. 
> Another question.  Is there a way to blur the experimental or density 
> modified phases when using mlhl target?
> Thanks.
> Jianghai
> +++++++++++++++++++++++++++++++
> Jianghai Zhu, Ph.D
> CBR Institute for Biomedical Research
> Department of Pathology
> Harvard Medical School
> 200 Longwood Ave., Boston, MA 02115
> Ph: 617-278-3211
> Fx: 618-278-3232
> +++++++++++++++++++++++++++++++
> ------------------------------------------------------------------------
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

Paul Adams
Senior Staff Scientist, Physical Biosciences Division
Head, Berkeley Center for Structural Biology
Deputy Principal Investigator, Berkeley Structural Genomics Center

Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.

More information about the phenixbb mailing list