you might have to specify something like remove_hydrogens=False HTH P Jianghai Zhu wrote:
Thanks. I will try that.
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 +++++++++++++++++++++++++++++++
On Mar 27, 2007, at 3:19 PM, Paul Adams wrote:
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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