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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: converting structure factor files to mtz files
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-01

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Date: 2007-11-01

Subject: Re: converting structure factor files to mtz files
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-01

Use the CCP4i Reflection utilities

Convert to MTZ and say you are importing mmCIF
It will sort it out for you

Eleanor

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 ? ? ?
> ? ? ? ? ? ?
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: converting structure factor files to mtz files
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-01

Next message:
Subject: Re: carving up maps (was re: pymol help)
From: Robert Esnouf robert {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-11-01