[phenixbb] refine

Phzwart phzwart at gmail.com
Tue Jun 7 18:21:41 PDT 2011


Hi Pavel,

How are centrics counted?

Peter


Op Jun 7, 2011 om 18:04 heeft Pavel Afonine <pafonine at lbl.gov> het volgende geschreven:

> Hi Martin,
> 
> I added a line to PDB file header that reports the number of Bijvoet pairs + singles (each pair {F+,F-} is counted as one reflection), so from now on you will get something like this:
> 
> REMARK   3
> REMARK   3  DATA USED IN REFINEMENT.
> REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.500
> REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 24.677
> REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 0.00
> REMARK   3   COMPLETENESS FOR RANGE        (%) : 98.35
> REMARK   3   NUMBER OF REFLECTIONS             : 31309
> REMARK   3   NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 16857
> REMARK   3
> 
> Similar change is made to phenix.model_vs_data output.
> 
> This will be available in next nightly build (which will be available in a day or two):
> 
> http://www.phenix-online.org/download/nightly_builds.cgi
> 
> version dev-780 and up.
> 
> Pavel.
> 
> 
> On 6/7/11 1:43 AM, MARTYN SYMMONS wrote:
>> Dear PHENIX guys
>>     as a side note to this:
>> 
>>     a continuing problem with anomalous data like this is that the header for deposition at the PDB gives statistics relating to the unmerged data - so that seems to consider the F(+) and F(-) as separate reflections. This is a bit misleading and somewhat at variance with usual crystallographic practice.
>> 
>>      It also makes it difficult to see easily what is the actual number of reflections refined against. In the best case it will be about half of the reported but I can't see how you can determine exactly without going to the data to see what proportion of both anomalous pairs were collected in each resolution range. It also inflates the count of Rfree data by the same factor - which gives a misleading impression.
>> 
>>     A workaround would be to redo the refinement at the end with the anomalous data merged and give the PDB those statistics. Presumably you will have to do this to give an analysis based on merged data for 'Table I' in the paper on the structure.
>> 
>>      All the best
>>           Martyn
>> 
>> 
>> 
>> 
>> 
>> 
>> --- On Mon, 6/6/11, Thomas C. Terwilliger<terwilliger at lanl.gov>  wrote:
>> 
>>> From: Thomas C. Terwilliger<terwilliger at lanl.gov>
>>> Subject: Re: [phenixbb] refine
>>> To: "Nora Cronin"<Nora.Cronin at icr.ac.uk>
>>> Cc: "PHENIX user mailing list"<phenixbb at phenix-online.org>
>>> Date: Monday, 6 June, 2011, 21:47
>>> Hi Nora,
>>> 
>>> I'm sorry for the trouble!
>>> 
>>> Here is the easy way out: extract the appropriate columns
>>> of data from
>>> your HG_28_scala3.mtz and make a new file with them. Then
>>> you won't need
>>> to specify any data columns and it should run:
>>> 
>>>    phenix.reflection_file_converter
>>> HG_28_scala3.mtz \
>>>       HG_28_ano_data.mtz --label="I_28(+)"
>>> --mtz-root-label="I_28"
>>> 
>>> 
>>> I would like to fix the underlying problem however...
>>> 
>>> I was not able to figure out what combination of data files
>>> you have that
>>> produced this ending. Normally AutoSol should print
>>> something like this at
>>> the end of this failed run:
>>> 
>>> -----------------------------------------
>>> AutoSol Input failed
>>> Sorry...could not figure out which data to use..
>>> For SAD datasets please enter one datafile
>>> ...if this is a MAD dataset please specify expt_type='mad'
>>> 
>>> ...to specify a particular set of data you can specify one
>>> of the
>>> following :
>>> 
>>> labels='F_28(+) SIGF_28(+) F_28(-) SIGF_28(-)'
>>> labels='I_28(+) SIGI_28(+) I_28(-) SIGI_28(-)'
>>> -----------------------------------------
>>> 
>>> In that case, adding one of the lines above should allow it
>>> to work.
>>> 
>>> In your case, autosol got beyond this point and has passed
>>> your data file
>>> on to phenix.refine, where it has given your error
>>> message:
>>> 
>>> "Multiple equally suitable arrays of observed xray data
>>> found."
>>> 
>>> I couldn't make this happen with some test datasets... so:
>>> can you
>>> possibly send me (off-list: terwilliger at lanl.gov) the files and inputs
>>> that led to this problem? Or if you would prefer, the
>>> AutoSol_run_1_1.log
>>> file?
>>> 
>>> Thanks!
>>> 
>>> All the best,
>>> Tom T
>>> 
>>> 
>>> 
>>> 
>>>>> I'm have a problem with mtz labels
>>>>> 
>>>>> Multiple equally suitable arrays of observed xray
>>> data found.
>>>>> Possible choices:
>>>>>    HG_28_scala3.mtz:IMEAN_28,SIGIMEAN_28
>>>>>    HG_28_scala3.mtz:I_28(+),SIGI_28(+),I_28(-),SIGI_28(-),merged
>>>>> 
>>>>> Please use refinement.input.xray_data.labels
>>>>> to specify an unambiguous substring of the target
>>> label.
>>>>> Sorry: Multiple equally suitable arrays of
>>> observed xray data found.
>>>>> I've listed all labels
>>>>> 
>>>>> Groups of input data:  [1]
>>>>> 
>>>>> NOTE: Deleting group  1  which has no
>>> data...
>>>>> closing overall log
>>> AutoSol_run_2_/AutoSol_run_2_1.log
>>> ---------------------------------------------------------------------------
>>>>> List of all anomalous datasets in
>>> HG_28_scala3.mtz
>>>>> 'F_28(+) SIGF_28(+) F_28(-) SIGF_28(-)'
>>>>> 'I_28(+) SIGI_28(+) I_28(-) SIGI_28(-)'
>>>>> 
>>>>> 
>>>>> List of all datasets in HG_28_scala3.mtz
>>>>> 'F_28 SIGF_28'
>>>>> 'F_28(+) SIGF_28(+) F_28(-) SIGF_28(-)'
>>>>> 'IMEAN_28 SIGIMEAN_28'
>>>>> 'I_28(+) SIGI_28(+) I_28(-) SIGI_28(-)'
>>>>> 
>>>>> 
>>>>> List of all individual labels in HG_28_scala3.mtz
>>>>> 'FreeR_flag'
>>>>> 'F_28'
>>>>> 'SIGF_28'
>>>>> 'F_28(+)'
>>>>> 'SIGF_28(+)'
>>>>> 'F_28(-)'
>>>>> 'SIGF_28(-)'
>>>>> 'DANO_28'
>>>>> 'SIGDANO_28'
>>>>> 'IMEAN_28'
>>>>> 'SIGIMEAN_28'
>>>>> 'I_28(+)'
>>>>> 'SIGI_28(+)'
>>>>> 'I_28(-)'
>>>>> 'SIGI_28(-)'
>>>>> 
>>>>> Suggested uses:
>>>>> USE:  autosol data file
>>>>> labels='F_28(+) SIGF_28(+) F_28(-) SIGF_28(-)'
>>>>> (program labels: ['I/F', 'sigI/sigF', 'I/F-',
>>> 'sigI/sigF-'])
>>>>> (suggested list: ['F_28(+)', 'SIGF_28(+)',
>>> 'F_28(-)', 'SIGF_28(-)'])
>>>>> USE:  autosol data file
>>>>> labels='I_28(+) SIGI_28(+) I_28(-) SIGI_28(-)'
>>>>> (program labels: ['I/F', 'sigI/sigF', 'I/F-',
>>> 'sigI/sigF-'])
>>>>> (suggested list: ['I_28(+)', 'SIGI_28(+)',
>>> 'I_28(-)', 'SIGI_28(-)'])
>>>>> USE:  autobuild/ligandfit/automr datafile
>>>>> input_labels='F_28 SIGF_28 None None None None
>>> None None FreeR_flag'
>>>>> (program labels: ['FP', 'SIGFP', 'PHIB', 'FOM',
>>> 'HLA', 'HLB', 'HLC',
>>>>> 'HLD', 'FreeR_flag'])
>>>>> (suggested list: ['F_28', 'SIGF_28', 'None',
>>> 'None', 'None', 'None',
>>>>> 'None', 'None', 'FreeR_flag'])
>>>>> 
>>>>> USE:  autosol/autobuild refinement file
>>>>> input_refinement_labels='F_28 SIGF_28 FreeR_flag'
>>>>> (program labels: ['FP', 'SIGFP', 'FreeR_flag'])
>>>>> (suggested list: ['F_28', 'SIGF_28',
>>> 'FreeR_flag'])
>>>>> USE:  autobuild map file
>>>>> input_map_labels='F_28 None None'
>>>>> (program labels: ['FP', 'PHIB', 'FOM'])
>>>>> (suggested list: ['F_28', 'None', 'None'])
>>>>> 
>>>>> USE:  automr labels to pass to autobuild
>>>>> input_label_string ='F_28 SIGF_28'
>>>>> (program labels: ['I/F', 'sigI/sigF'])
>>>>> (suggested list: ['F_28', 'SIGF_28'])
>>>>> 
>>>>> USE:  automr labels to pass to autobuild
>>>>> input_label_string ='IMEAN_28 SIGIMEAN_28'
>>>>> (program labels: ['I/F', 'sigI/sigF'])
>>>>> (suggested list: ['IMEAN_28', 'SIGIMEAN_28'])
>>>>> 
>>>>> No combination is accepted
>>>>> 
>>>>> Seems obvious but I can't solve it.
>>>>> 
>>>>> Thanks
>>>>> 
>>>>> 
>>>>> Nora
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On 2 Jun 2011, at 14:32, Thomas C. Terwilliger
>>> wrote:
>>>>>> Hi Jianghai,
>>>>>> 
>>>>>> Thanks for the request!  All the phenix
>>> tools use the same
>>>>>> reflection_file_reader, so each should be able
>>> to read XDS files,
>>>>>> including phenix.autosol.  If that does
>>> not seem to be the case, I'll be
>>>>>> happy to look into it if you can send me the
>>> first few hundred lines of
>>>>>> a
>>>>>> data file that does not work properly.
>>>>>> 
>>>>>> All the best,
>>>>>> Tom T
>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> In the manual of version 1.7.1, I
>>> found out that only phenix.hyss can
>>>>>>>> read
>>>>>>>> XDS_ASCII files with merged
>>> data.  Do other phenix tools recognized
>>>>>>>> XDS_ASCII files?  If not, I would
>>> like to request this feature.  For
>>>>>>>> example, let phenix.autosol read
>>> XDS_ASCII file with merged or
>>>>>>>> unmerged
>>>>>>>> data.
>>>>>>>> 
>>>>>>>> Thanks.
>>>>>>>> 
>>>>>>>> -- Jianghai
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
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>>>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>>>>> 
>>>>>> 
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>>>>> X-Ray Laboratory Manager
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>>> 5445
>>>>> Section of Structural Biology
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>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
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