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

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

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

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

Next message:
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

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

Dear Bjoern,

this is a problem with several newer mmcif files in the PDB. There
are many items in the cif-file which are not in the CCP4 library.
This is a bit annoying when you want to convert large numbers
of mmcifs to mtzs for whatever reason, but I guess the only
solution is to wait until the CCP4 guys have updated their
dictionaries.

Cheers, Manfred.

********************************************************************
* *
* Dr. Manfred S. Weiss *
* *
* Team Leader *
* *
* EMBL Hamburg Outstation Fon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg Email: msweiss@embl-hamburg.de *
* GERMANY Web: www.embl-hamburg.de/~msweiss/ *
* *
********************************************************************

On Tue, 6 Nov 2007, [ISO-8859-1] Björn Kauppi wrote:

> 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/ *
> > ***********************************************************************
>
>
> ***************************************************************************
> This e-mail may contain confidential information proprietary to Karo Bio AB
> and is meant for the intended addressee(s) only. Any unauthorized review,
> use, disclosure or distribution is prohibited. If you have received this
> message in error, please advise the sender and delete the e-mail and any
> attachments from your files. Thank you!
> ***************************************************************************
>

CCP4bb navigation

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

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

Next message:
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