From M.D.Winn@dl.ac.uk Mon Aug 1 13:25:52 2005 Date: Mon, 1 Aug 2005 09:52:23 +0100 From: Martyn Winn To: Peter Briggs Cc: Kim Henrick Subject: Re: mtz2various question (fwd) This is the last correspondence I had on this. As you see, Jawahar had suggested generic tokens. But I didn't implement this. I was (still am) confused as to who has authority to decide these things. If you can get agreement between EBI and RCSB, and fix mtz2various, that would be great. I have no opinions of my own on this. You'll see, there was also the issue of multiple datasets within one file. Good luck! m On Thu, 5 Jun 2003, Jawahar Swaminathan wrote: > Kim, Martyn, > > I think we should dispense with the specific information in the form of > SAD,MAD or ccp4 in the cif items in order to make them more generic. > > I would therefore, think that the following items should be > > > _refln.F_meas_plus > _refln.F_meas_plus_sigma > _refln.F_meas_minus > _refln.F_meas_minus_sigma > > _refln.intensity_meas_plus > _refln.intensity_meas_plus_sigma > _refln.intensity_meas_minus > _refln.intensity_meas_minus_sigma > > How does that sound ? > > Jawahar > > > Kim Henrick wrote: > > >Jawahar > > > >can you answer this > >about the original question > >on extra mtz items / mmcif > > > >kim > > > >Kim HENRICK henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629 > > > >---------- Forwarded message ---------- > >Date: Sat, 31 May 2003 03:51:31 +0100 > >From: Martyn Winn > >To: Kim Henrick > >Cc: m.d.winn@dl.ac.uk, jawahar@ebi.ac.uk, gerard@xray.bmc.uu.se, > > jwest@rcsb.rutgers.edu > >Subject: Re: mtz2various question > > > > > >All is possible in mtz2various. I just wonder what > >is desirable ... > > > >My original questions boil down to: > >1) is yuor requested change from storing anomalous > >as hkl/-h-k-l to storing (+) (-) columns acceptable > >to all? > >2) should the item names really include "SAD" or be more > >generic? > > > >Yes, MTZ can contain several crystals (each with > >own cell dims). Crystal can contain several datasets. > >Dataset can contain several columns. Can output as > >you suggest if that is acceptable to all. It is not > >done yet as was illegal cif, but would be relatively > >easy (apart from dealing with god-awful Fortran > >program ...) > > > >But mtz2various doesnt know where columns come from. > >SO have to rely on user input to say if SAD/MIR. > >Same point for column refined against. That should > >come directly from Refmac. We can prompt user within > >Data Harvesting Management Tool. Or maybe read from > >refmac log file / harvest file and forward to > >mtz2various. > > > >Many ways to skin this cat. Just tell me how > >tortuous an mmcif file would still be acceptable, > >and well do it. > > > >m > > > > > >On Tue, 27 May 2003, Kim Henrick wrote: > > > > > > > >>Martyn > >> > >> > >>re mtz2various options > >> > >>as the current mtz ccp4 holds multiple cells/per dataset > >>in the header > >> > >>is there an option to o/p in a single mmcif file for > >>structure factors several datasets > >> > >>as there are among other data > >> CRYSTAL ID of dataset (Integer) > >> DATASET ID of dataset (Integer) > >> DCELL ID of dataset (Integer) > >> DWAVEL ID of dataset (Integer) > >> NDIF > >>with hkl column COL keyword a "dataset ID" > >> COL > >> Column Label (Character*30) > >> Column Type (Character*1) for each column > >> Minimum and Maximum value in each column (Real) > >> ID of corresponding dataset (Integer) > >> > >>is options to say several datasets o/p and no other keywords > >>so that one can get something like > >> > >>loop_ > >>_exptl_crystal.id > >>1 > >>2 > >>3 > >> > >>loop_ > >>_diffrn_radiation.crystal_id # not offical cif > >>_diffrn_radiation.diffrn_id > >>_diffrn_radiation.wavelength_id > >>_diffrn_radiation.details > >>1 1 1 'Dataset Name (Character*64)' > >>2 2 2 > >>3 3 3 > >> > >> > >># officially there is no link directly from cell to _exptl_crystal.id > >># cell is based on entry id so one cell per entry > >># this is artificial > >> > >>loop_ > >>_cell.crystal_id # not offical cif > >>_cell.angle_alpha > >>_cell.angle_beta > >>_cell.angle_gamma > >>_cell.length_a > >>_cell.length_b > >>_cell.length_c > >> 1 .... stuff ... > >> 2 > >> 3 > >> > >>loop_ > >>_diffrn_radiation_wavelength.id > >>_diffrn_radiation_wavelength.wavelength > >>1 ... > >>2 ... > >>3 ... > >> > >> > >># general comments refer to the hkl used in refinement only linked by entry_id > >># but need a marker to show which dataset refers to coordinate refinement > >># this loop would only have one row but it looks better as a loop > >> > >>loop_ > >>_reflns.entry_id > >>_reflns.crystal_id # not official cif > >>_reflns.d_resolution_high > >>_reflns.d_resolution_low > >>_reflns.number_all > >>1abc 2 2.596 28.630 10491 > >> > >># usually just as is > >>loop_ > >>_reflns_scale.group_code > >>1 > >> > >># more un-official cif needs crystal_id > >> > >>loop_ > >>_symmetry.entry_id > >>_symmetry.crystal_id # not official cif > >>_symmetry.space_group_name_H-M > >>1abc 2 'C 1 2 1' > >> > >>loop_ > >>_symmetry.crystal_id # not official cif > >>_symmetry_equiv.id > >>_symmetry_equiv.pos_as_xyz > >> 2 1 'X,Y,Z' > >> 2 2 '-X,Y,-Z' > >> 2 3 '1/2+X,1/2+Y,Z' > >> 2 4 '1/2-X,1/2+Y,-Z' > >> > >> > >>loop_ > >> _refln.wavelength_id Always written > >> _refln.crystal_id Always written > >> _refln.scale_group_code Always written > >> _refln.index_h Always written > >> _refln.index_k Always written > >> _refln.index_l Always written > >> _refln.status Always written > >> > >>then columns from the mtz file per dataset id using crysal_id as dataset id > >> > >> > >>John is this possible - how illegal is this in mmcif? > >> > >> > >>(this is apart from a soon to be requested map coefficient tag) > >> > >>it is now a common request to deposit multiple datasets > >> > >>kim > >> > >> > >> > >> > >> > >> > >> > > > >************************************************************************** > >* * > >* Dr. Martyn Winn * > >* * > >* Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND * > >* Tel: +44 1925 603455 E-mail: m.d.winn@dl.ac.uk (personal) * > >* Fax: +44 1925 603124 E-mail: ccp4@dl.ac.uk (CCP4 problems) * > >* URL: http://www.dl.ac.uk/CCP/CCP4/martyn/martyn.html * > >************************************************************************** > > > > > > > > > ************************************************************************** * * * Dr. Martyn Winn * * * * Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND * * Tel: +44 1925 603455 E-mail: m.d.winn@ccp4.ac.uk (personal) * * Fax: +44 1925 603825 E-mail: ccp4@ccp4.ac.uk (CCP4 problems) * * URL: http://www.ccp4.ac.uk/martyn/martyn.html * **************************************************************************