Completeness issue by phenix

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Young-Jin Cho

15 Dec 2008 15 Dec '08

3:39 p.m.

Hi, I was happy for using phenix but am struggling with a strange result on completeness calculation. One typical data set I used kept showing low completeness, so I used the same mtz, and pdb file on Refmac: it turned out has more than 98% whereas phenix.refine gave me about 46% completeness. I have slightly lower value of R but higher Rfree from phenix calculation without adding H atoms. I don't know if this is a bug or a problem on my data set (hopefully not). thanks in advance, YoungJin

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Ralf W. Grosse-Kunstleve

15 Dec 15 Dec

3:59 p.m.

Hi YoungJin, I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this: ================================== X-ray data ================================= F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X R-free flags: 1yjp.mtz:R-free-flags Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here If you see "Anomalous flag: True" try adding this to the phenix.refine command line: xray_data.force_anomalous_flag_to_be_equal_to=False Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated. Ralf

Rupert Russell

4:44 p.m.

Dear Ralf, I too have experienced this issue many times before. My .mtz files were generated through the ccp4i "import merged data" tab (default parameters), after the data were processed with scalepack. Letting phenix use the .sca file instead overcomes this but this is not an ideal situation for cross-compatibility between different programs. Cheers Rupert Russell Ralf W. Grosse-Kunstleve wrote:

...

Hi YoungJin,

I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this:

================================== X-ray data =================================

F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X

R-free flags: 1yjp.mtz:R-free-flags

Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here

If you see "Anomalous flag: True" try adding this to the phenix.refine command line:

xray_data.force_anomalous_flag_to_be_equal_to=False

Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated.

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Engin Ozkan

4:52 p.m.

I believe the default in scalepack2mtz in ccp4i is Anomalous on. That clearly explains your observations. You should consider Ralf's point that the data might have been converted to mtz with separate Friedel pairs, even though it was scaled initially as not. Engin ----- Original Message ----- From: "Rupert Russell" To: "Ralf W. Grosse-Kunstleve" , "PHENIX user mailing list" Sent: Monday, December 15, 2008 10:44:03 AM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] Completeness issue by phenix Dear Ralf, I too have experienced this issue many times before. My .mtz files were generated through the ccp4i "import merged data" tab (default parameters), after the data were processed with scalepack. Letting phenix use the .sca file instead overcomes this but this is not an ideal situation for cross-compatibility between different programs. Cheers Rupert Russell Ralf W. Grosse-Kunstleve wrote:

...

Hi YoungJin,

I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this:

================================== X-ray data =================================

F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X

R-free flags: 1yjp.mtz:R-free-flags

Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here

If you see "Anomalous flag: True" try adding this to the phenix.refine command line:

xray_data.force_anomalous_flag_to_be_equal_to=False

Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated.

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Ralf W. Grosse-Kunstleve

5:11 p.m.

...

I too have experienced this issue many times before. My .mtz files were generated through the ccp4i "import merged data" tab (default parameters), after the data were processed with scalepack. Letting phenix use the .sca file instead overcomes this but this is not an ideal situation for cross-compatibility between different programs.

Thanks for explaining the situation. It hope I can find a way to automatically detect that there are in fact no anomalous data. Could you send me an example pair of .sca and .mtz files? (I don't have ccp4i easily available.) Ralf

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Engin Ozkan
Ralf W. Grosse-Kunstleve
Rupert Russell
Young-Jin Cho