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).
Cheers,
Paul
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
+++++++++++++++++++++++++++++++
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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.
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