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

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

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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

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Subject: Re: libccp4map.so
From: P J Briggs p {- dot -} j {- dot -} briggs {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-06

Subject: Re: converting structure factor files to mtz files
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-06

You need to update to CCP4 6.0.2, these items are now recognised.

We try to keep up with the latest cif definitions, but there is a lag.
The documentation for cif2mtz lists the column labels recognised. These are
only labels, so if the worst comes to the worst, you can edit these
in the cif file to something that cif2mtz recognises (as long as it is the
same type of column!!)

HTH
Martyn

-----Original Message-----
From: Björn Kauppi [mailto:bjorn.kauppi@karobio.se]
Sent: Tue 11/6/2007 10:16 AM
To: Winn, MD (Martyn); CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] converting structure factor files to mtz files

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

Next message:
Subject: Re: libccp4map.so
From: P J Briggs p {- dot -} j {- dot -} briggs {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-06