Re: [ccp4bb] converting structure factor files to mtz files

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CCP4bb <-- 2007 <-- November 2007 <-- 06 November 2007

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From: Ronnie Berntsson r {- dot -} berntsson {- at -} RUG {- dot -} NL
Date: 2007-11-06

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Subject: Re: converting structure factor files to mtz files
From: "Manfred S {- dot -} Weiss" msweiss {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-11-06

Subject: Re: converting structure factor files to mtz files
From: _Björn_Kauppi_ bjorn {- dot -} kauppi {- at -} KAROBIO {- dot -} SE
Date: 2007-11-06

Hi,
I also have problems running cif2mtz using ccp4i (5.99) interface with several mmCIF files downloaded from the pdb (e.g., 2pip, ) on my linux box.
Problems with the _refln.pdbx_F_plus etc cards it seems:
Files without anomalous data work.

--snip from log file:
Line 58: data name "_refln.pdbx_F_plus" not present in dictionary

Line 59: data name "_refln.pdbx_F_plus_sigma" not present in dictionary

Line 60: data name "_refln.pdbx_F_minus" not present in dictionary

Line 61: data name "_refln.pdbx_F_minus_sigma" not present in dictionary

Line 62: data name "_refln.pdbx_anom_difference" not present in dictionary

Line 63: data name "_refln.pdbx_anom_difference_sigma" not present in dictionary

Line 64: data name "_refln.pdbx_I_plus" not present in dictionary

Line 65: data name "_refln.pdbx_I_plus_sigma" not present in dictionary

Line 66: data name "_refln.pdbx_I_minus" not present in dictionary

Line 67: data name "_refln.pdbx_I_minus_sigma" not present in dictionary

--- CIF opened read-only for input ---
The file contains the following data blocks:
data_r2piusf (at line 1)

>>>> CCIF signal CCIF_CATNOTCOMPLETE (severity: Warning) <<<<
(Raised in new_context)
Could not open context on category 'refln'; item '_refln.pdbx_F_plus' not defined in dictionary!

cif2mtz: Error in ccp4ccif_setup_context: Unexpected context type for category REFLN
Times: User: 0.6s System: 0.0s Elapsed: 0:00

Björn Kauppi

> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Martyn Winn
> Sent: den 1 november 2007 10:14
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] converting structure factor files to mtz files
>
> The first 3 cif columns are not the problem. cif2mtz will happily skip
> these along with any other items it doesn't explicitly deal with.
>
> The problem is simply the extra columns F(+) etc, yes?
>
> This bug has been seen on Windows. The same job should work fine on
> Linux or Macs. Or you should be able to simply delete these spurious
> columns with cad, sftools, etc
> I'm sure this will be easier than playing with Fortran formatting ....
>
> The bug is somewhere in the depths of the cif library, and we don't have
> a fix yet.
>
> HTH
> Martyn
>
> On Wed, 2007-10-31 at 19:49 -0400, Zheng Zhou wrote:
> > Hi,
> >
> > Could anyone give a quick hint for the Fortran format for the
> > following structure factor mmCIF file? or Is there any easy program or
> > better way to convert it? I think I need to skip first 3 columns.
> >
> > Thanks in advance.
> >
> > Joe
> >
> > loop_
> > _refln.crystal_id
> > _refln.wavelength_id
> > _refln.scale_group_code
> > _refln.index_h
> > _refln.index_k
> > _refln.index_l
> > _refln.F_meas_au
> > _refln.F_meas_sigma_au
> > _refln.status
> > 1 1 1 2 0 0 617.50 5.41 o
> > 1 1 1 4 0 0 773.50 6.92 o
> > 1 1 1 6 0 0 62.30 3.19 o
> >
> > I am trying to view the electron density of a published structure. I
> > downloaded the file from pdb and used cif2mtz in ccp4. I think the
> > following output mtz is wrong.
> >
> > * Column Labels :
> >
> > H K L FREE FP SIGFP F(+) SIGF(+) F(-) SIGF(-) DP SIGDP I(+) SIGI(+)
> > I(-) SIGI(-)
> >
> > * Column Types :
> >
> > H H H I F Q G L G L D Q K M K M
> >
> > * Associated datasets :
> >
> > 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1
> >
> > * Cell Dimensions : (obsolete - refer to dataset cell dimensions
> > above)
> >
> > 88.0800 86.3600 80.7700 90.0000 95.7100 90.0000
> >
> > * Resolution Range :
> >
> > 0.00045 0.29217 ( 47.298 - 1.850 A )
> >
> > * Sort Order :
> >
> > 1 2 3 0 0
> >
> > * Space group = 'C 1 2 1' (number 5)
> >
> >
> >
> > OVERALL FILE STATISTICS for resolution range 0.000 - 0.292
> > =======================
> >
> >
> > Col Sort Min Max Num % Mean Mean Resolution
> > Type Column
> > num order Missing complete abs. Low High
> > label
> >
> > 1 ASC -47 47 0 100.00 -1.4 17.9 47.28
> > 1.85 H H
> > 2 NONE 0 46 0 100.00 17.2 17.2 47.28 1.85
> > H K
> > 3 NONE 0 43 0 100.00 16.4 16.4 47.28 1.85
> > H L
> > 4 NONE 0.0 19.0 0 100.00 9.52 9.52 47.28
> > 1.85 I FREE
> > 5 NONE 0.0 1566.0 50 99.90 162.85 162.85 47.28 1.85
> > F FP
> > 6 NONE 0.0 82.1 50 99.90 9.49 9.49 47.28 1.85
> > Q SIGFP
> > 7 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > G F(+)
> > 8 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > L SIGF(+)
> > 9 BOTH ? ? 51373 0.00 ? ? - 999.00
> > 0.00 G F(-)
> > 10 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > L SIGF(-)
> > 11 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > D DP
> > 12 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > Q SIGDP
> > 13 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > K I(+)
> > 14 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > M SIGI(+)
> > 15 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > K I(-)
> > 16 BOTH ? ? 51373 0.00 ? ? -999.00 0.00
> > M SIGI(-)
> >
> >
> > No. of reflections used in FILE STATISTICS 51373
> >
> >
> >
> > LIST OF REFLECTIONS
> > ===================
> >
> > -47 1 1 0.00 0.00
> > 0.00 ? ? ?
> > ? ? ? ? ?
> ?
> > ?
> > -47 1 2 0.00 0.00
> > 0.00 ? ? ?
> > ? ? ? ? ?
> ?
> > ?
> > -47 1 3 17.00 0.00
> > 0.00 ? ? ?
> > ? ? ? ? ?
> ?
> --
> ***********************************************************************
> * *
> * Dr. Martyn Winn *
> * *
> * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
> * Tel: +44 1925 603455 E-mail: m.d.winn@dl.ac.uk *
> * Fax: +44 1925 603825 Skype name: martyn.winn *
> * URL: http://www.ccp4.ac.uk/martyn/ *
> ***********************************************************************

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CCP4bb <-- 2007 <-- November 2007 <-- 06 November 2007

Previous message:
Subject: Re: Apple OS 10.5 and X11
From: Ronnie Berntsson r {- dot -} berntsson {- at -} RUG {- dot -} NL
Date: 2007-11-06

Next message:
Subject: Re: converting structure factor files to mtz files
From: "Manfred S {- dot -} Weiss" msweiss {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-11-06