[phenixbb] riding hydrogen and mlhl

[Jianghai Zhu]

Just tried the phenix.reduce as Paul suggested.  I used  
"phenix.reduce -build -flips old.pdb > new.pdb" to generate all the H  
atoms.  Then I fed the new.pdb to phenix.refine with  
"remove_hydrogens=False". The refinement included individual_sites 
+individual_adp+tls.  I compared the results from with/without H  
atoms.  Without H atoms: R=0.2369, Rfree=0.2876; with H atoms:  
R=0.2363, Rfree=0.2911.  I didn't see much improvement here.  Did I  
miss something?  Of course, I understand this is still at the early  
stage of development.

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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>
> -- 
> 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/
>
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