Re: [phenixbb] refine

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 wrote:

From: Thomas C. Terwilliger Subject: Re: [phenixbb] refine To: "Nora Cronin" Cc: "PHENIX user mailing list" 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: [email protected])  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

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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

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List of all anomalous datasets in

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'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:

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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

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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

HG_28_scala3.mtz like to request this feature.  For

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example, let phenix.autosol read XDS_ASCII file with merged or unmerged data.

Thanks.

-- Jianghai

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