[phenixbb] refine

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Jun 6 13:47:56 PDT 2011 

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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> 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
>>
>> Dr N B Cronin
>> X-Ray Laboratory Manager               Tel. (+44) 020 7153 5445
>> Section of Structural Biology             Fax. (+44) 020 7153 5457
>> Chester Beatty Laboratories		mobile: (+44) 07787554059
>> The Institute of Cancer Research
>> 237 Fulham Road
>> London
>> SW3 6JB
>>
>>
>>
>>
>>
>>
>>
>> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
>> Company Limited by Guarantee, Registered in England under Company No.
>> 534147 with its Registered Office at 123 Old Brompton Road, London SW7
>> 3RP.
>>
>> This e-mail message is confidential and for use by the addressee only.  If
>> the message is received by anyone other than the addressee, please return
>> the message to the sender by replying to it and then delete the message
>> from your computer and network.

More information about the phenixbb mailing list