[phenixbb] riding hydrogen and mlhl

[Peter Zwart]

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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>>>
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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
>> http://cci.lbl.gov/
>>
>> Lawrence Berkeley Laboratory
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>> BLDG 64R0121
>> Berkeley, CA 94720, USA.
>> --
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> 
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