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Re: [ccp4bb] converting structure factor files to mtz files |
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CCP4bb navigationCCP4bb <-- 2007 <-- November 2007 <-- 01 November 2007Subject: 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 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/ * *********************************************************************** CCP4bb navigationCCP4bb <-- 2007 <-- November 2007 <-- 01 November 2007 |
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