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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-- 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 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. -- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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 +++++++++++++++++++++++++++++++

--------------------------------------------------------------------- ---

_______________________________________________ phenixbb mailing list [email protected] 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 http://cci.lbl.gov/

Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. -- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb