[phenixbb] refine
MARTYN SYMMONS
martainn_oshiomains at btinternet.com
Wed Jun 8 01:28:31 PDT 2011
Thanks Pavel
that's great - I appreciate it -
all the best
Martyn
--- On Wed, 8/6/11, Pavel Afonine <pafonine at lbl.gov> wrote:
> From: Pavel Afonine <pafonine at lbl.gov>
> Subject: Re: [phenixbb] refine
> To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
> Cc: "MARTYN SYMMONS" <martainn_oshiomains at btinternet.com>
> Date: Wednesday, 8 June, 2011, 2:04
> 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
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >> _______________________________________________
> >>>>>>> phenixbb mailing list
> >>>>>>> phenixbb at phenix-online.org
> >>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
> >>>>>>>
> >>>>>
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> >>>>> http://phenix-online.org/mailman/listinfo/phenixbb
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