An MTZ file contains the space group name, space group number, and all the symmetry operators. Space group numbers such as 4005 are an unofficial undocumented extension to International Tables rules and shouldn't be used as reliable information. The name or the operators should take precedence
Does Refmac really rely on the space group number, or it in some script/interface? Phil > Ian, > > I think I found the issue just by looking through mtzdmp output, but > there was a clue from the response I got yesterday: > > Hi Paul, > > I have come across this problem before, suddenly what was complete > data is only 50% complete. I seem to recall its because I2 is also > called space group 5 (same as C2), which confuses some programs. > > I tracked spacegroup number in the mtz headers. Pointless, aimless, > ctruncate use 4005 for I2. After Phaser (v 2.5.7), the spacegroup number > is just 5. That seemed to be the thing that is bothering refmac and > phenix.refine. For whatever reason I was using the phaser output for the > initial refinement. > > --paul > > > On 11/04/2016 10:58 AM, Ian Tickle wrote: >> >> Paul, mtzdump may not give the full header. The best way to get this >> is to use a text editor on the MTZ file (yes I know it looks like >> garbage!), scroll to the end where you will find the header starting >> at 'VERS MTZ:V1.1'. Then copy/paste everything from there to the end >> (don't worry about formatting it). >> >> Hopefully this will give a clue. >> >> Cheers >> >> -- Ian >> >> >> On 4 November 2016 at 14:49, Ian Tickle <ianj...@gmail.com >> <mailto:ianj...@gmail.com>> wrote: >> >> >> Hi Paul >> >> I just tried Refmac 5.8.0135 (which must be very similar to the >> version you are using) with an I2 dataset and I don't see this >> "conversion to C2". I doubt very much that the refinement >> programs need to convert to C2: I'm pretty sure they can do the >> refinement perfectly well in I2. >> >> I think it's much more likely that your MTZ header has somehow got >> corrupted with inconsistent space group info so you need to track >> back in the history list in the MTZ header and see which program >> was responsible for the corruption. Can you post the MTZ header >> so we can see the history list and the cell/space group info? >> >> Cheers >> >> -- Ian >> >> >> On 4 November 2016 at 14:39, Paul Paukstelis >> <shocksofmig...@gmail.com <mailto:shocksofmig...@gmail.com>> wrote: >> >> Refmac and phenix.refine versions I used both seem to be >> problematic. Both are I2 in and C2 out. >> >> --p >> >> On 11/04/2016 08:25 AM, Ian Tickle wrote: >>> >>> Hi Paul >>> >>> This sounds like there might be a recently-introduced bug >>> which should be reported to the author. I have several >>> structures in I2 & I haven't noticed anything like this. Can >>> you tell which program is introducing this error, e.g. by >>> looking at the mtzdump outputs? >>> >>> Cheers >>> >>> -- Ian >>> >>> >>> On 4 November 2016 at 12:00, Paul Paukstelis >>> <shocksofmig...@gmail.com <mailto:shocksofmig...@gmail.com>> >>> wrote: >>> >>> Thanks to all that responded. I sorted this out. >>> >>> It all appears to stem from the C2->I2 conversion. >>> Forcing everything in processing to stick with C2 fixes >>> all the issues! >>> >>> >>> Thanks again, >>> >>> --paul >>> >>> >>> >>> On 11/03/2016 12:39 PM, Paul Paukstelis wrote: >>> >>> CCP4BB, >>> >>> I posted some time back about a DNA oligonucleotide >>> structure we were working on. I had difficulty >>> phasing it despite strong signal from bromines, but >>> finally managed to get reasonable enough maps from a >>> few datasets to build, only to find that despite the >>> density looking quite good, it simply wouldn't refine >>> past R/Rfree of around 28/32. With help from ccp4bb >>> it began to become clear that this might be a >>> candidate for a lattice with translocation defects. >>> >>> I had my student make a variant in which two 3' >>> nucleotides that weren't involved in base pairing >>> contacts were removed. This crystallized under the >>> same conditions in a different space group and was >>> now diffracting to ~1.0 A (from about 2.2 in the >>> previous space group). Images overall looked good, >>> though we collected on some crystals that clearly had >>> more than one lattice that made indexing more >>> difficult. The best looking data still had some tails >>> on spots, but was easily indexed in C2, which >>> Pointless quite happily changed to I2 to minimize the >>> beta angle. There are no clear alternating >>> strong/weak intensities. Phaser finds a strong >>> solution using the previously built dimer, but notes >>> a 25% over origin peak in native Patterson. Maps look >>> very good, though after the first round of refinement >>> it is apparent that there is another dimer in the >>> ASU, but it is clearly overlapping the first. If I'm >>> not mistaken, all these clues suggest lattice >>> translocation defects. Question 1: any thoughts on >>> how likely it would be for a molecule to >>> intrinsically pack in such a way that it results in >>> lattice translocation defects? >>> >>> I thought it would be worthwhile pressing on given >>> the high resolution it would be possible to do >>> grouped occupancy refinement of the dimers without >>> taking too huge a hit in observation/parameters. >>> Refinement with refmac using occupancy groups leads >>> to a best R/Rfree of 18/24, though geometry could be >>> better in some spots. Curiously, refmac (or >>> phenix.refine) in the PDB header reports only 50% >>> completeness in the resolution range, though all the >>> data reduction and analysis (aimless, xtriage) report >>> 99% completeness. Question 2: Why is this? Phenix >>> logfile says something about removing about half the >>> reflections as systematic absences. I have been >>> working with everything in I2 after Pointless >>> switched it over. >>> >>> Question 3: Any other suggestions on how to proceed >>> with refinement in a case like this? My gut instinct >>> tells me that it would be better to not do intensity >>> correction due to the high resolution, but perhaps >>> that's something to pursue? >>> >>> Thank you in advance. >>> >>> --paul >>> >>> >> >> >> > >
