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: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * ******************************************************************** On Tue, 6 Nov 2007, [ISO-8859-1] Bj?rn 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! > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > cif2mtz: Error in ccp4ccif_setup_context: Unexpected context type for > category REFLN > Times: User: 0.6s System: 0.0s Elapsed: 0:00 > </pre> > </html> > <!--SUMMARY_END--></FONT></B> > > > Bj?rn Kauppi > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] 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: [EMAIL PROTECTED] * > > * 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! > *************************************************************************** >
