Completeness issue by phenix - revisited
Hi,
I'm having a problem using phenix.refine with my x-ray data. My
completeness is always 89% when it should be 99%. My data was originally
processed with CCP4i. I found an old post (see below) with a potential fix
that doesn't work for me. I've tried changing the 'Anomalous flag: True' to
'Anomalous flag: False' but my completeness is still 89%. I've clicked
through a variety of other setting in the GUI that I thought would help but
no luck. Does anyone have any ideas?
Thanks in advance,
Jon
----- Original Message -----
From: "Ralf W. Grosse-Kunstleve"
Could it be that you reserved 10% of your data for Rfree and are looking at the completeness for the work set? Do you have an I/sigma(I) cutoff that is high? If not, it might help to post the some of the Phenix output, e.g., the table with the completeness data along with the resolution limits, etc. Best - MM On Feb 3, 2010, at 10:42 PM, J. Fleming wrote:
Hi,
I'm having a problem using phenix.refine with my x-ray data. My completeness is always 89% when it should be 99%. My data was originally processed with CCP4i. I found an old post (see below) with a potential fix that doesn't work for me. I've tried changing the 'Anomalous flag: True' to 'Anomalous flag: False' but my completeness is still 89%. I've clicked through a variety of other setting in the GUI that I thought would help but no luck. Does anyone have any ideas?
Thanks in advance, Jon
----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
To: phenixbb at phenix-online.org Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Completeness issue by phenix
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
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Hi Jon, please run phenix.model_vs_data mode.pdb data.mtz and that will give the the numbers for data completeness. Please send me the output of the above command if it doesn't clarify this issue. Let me know if you have any questions. Pavel. On 2/3/10 7:48 PM, Mischa Machius wrote:
Could it be that you reserved 10% of your data for Rfree and are looking at the completeness for the work set? Do you have an I/sigma(I) cutoff that is high? If not, it might help to post the some of the Phenix output, e.g., the table with the completeness data along with the resolution limits, etc. Best - MM
On Feb 3, 2010, at 10:42 PM, J. Fleming wrote:
Hi,
I'm having a problem using phenix.refine with my x-ray data. My completeness is always 89% when it should be 99%. My data was originally processed with CCP4i. I found an old post (see below) with a potential fix that doesn't work for me. I've tried changing the 'Anomalous flag: True' to 'Anomalous flag: False' but my completeness is still 89%. I've clicked through a variety of other setting in the GUI that I thought would help but no luck. Does anyone have any ideas?
Thanks in advance, Jon
----- Original Message ----- From: "Ralf W. Grosse-Kunstleve"
http://www.phenix-online.org/mailman/listinfo/phenixbb> To: phenixbb at phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Completeness issue by phenix
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
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participants (3)
-
J. Fleming -
Mischa Machius -
Pavel Afonine