[phenixbb] Completeness issue by phenix - revisited

Pavel Afonine PAfonine at lbl.gov
Wed Feb 3 21:31:41 PST 2010


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" <rwgk at cci.lbl.gov <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
>>     
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100203/eda36269/attachment-0003.htm>


More information about the phenixbb mailing list