Re: [phenixbb] refine

8 Jun 2011

      Thanks Pavel 
           that's great - I appreciate it -
             all the best 
                   Martyn 

--- On Wed, 8/6/11, Pavel Afonine  wrote:
...
From: Pavel Afonine 
Subject: Re: [phenixbb] refine
To: "PHENIX user mailing list" 
Cc: "MARTYN SYMMONS" 
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.
...
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
On 6/7/11 1:43 AM, MARTYN SYMMONS wrote:
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
...
...
of data from
your HG_28_scala3.mtz and make a new file with
...
...
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
columns
them. Then
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
...
...
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
...
Hi Jianghai,
Thanks for the request!  All the
...
reflection_file_reader, so each should
be able
to read XDS files,
including phenix.autosol.  If
...
happy to look into it if you can send
me the
first few hundred lines of
a
data file that does not work
On 2 Jun 2011, at 14:32, Thomas C.
Terwilliger
wrote:
phenix
tools use the same
that does
not seem to be the case, I'll be
properly.
...
All the best,
Tom T
>> Hi,
>>
>> In the manual of version
...
>> read
>> XDS_ASCII files with merged
data.  Do other phenix tools recognized
>> XDS_ASCII files?  If not,
I would
1.7.1, I
found out that only phenix.hyss can
like to request this feature.  For
...
>> example, let phenix.autosol
read
XDS_ASCII file with merged or
>> unmerged
>> data.
>>
>> Thanks.
>>
>> -- Jianghai
>>
>>
>>
>>
>>

...
...
...
>> phenixbb mailing list
>> [email protected]
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>

...
...
...
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Dr N B Cronin
X-Ray Laboratory Manager
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(+44) 020 7153
5445
Section of Structural Biology
         Fax. (+44)
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