Not sure I fully understand. Are we really talking about non-crystallographer scientists, often willing to understand how a biologically meaningful molecule / entity looks like? Are these non-crystallographers really interested in crystal packing issues? Is it so much difficult to press on a couple of buttons in the program with which you do open your coordinates to generate the symmetry related molecules? I am feeling we are a bit off here...
Leo > On 29 Jan 2016, at 20:52, Quyen Hoang <qqho...@gmail.com> wrote: > > Sure, but you would need to expand space group X in order to see the > intermolecular interactions that would have been seen in P1. Also, it is > often discussed here about how non-crystallographers might use our structural > models deposited in the PDB, I doubt that many of them would know how to > expand. > > I am not advocating, just discussing. > > Cheers, > Quyen > > Sent from my BlackBerry 10 smartphone. > From: Keller, Jacob > Sent: Friday, January 29, 2016 2:20 PM > To: Quyen Hoang; CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] Spacegroups, screw axes and ordering > > >I mean, would it not be more informative to have a P1 unit cell filled with > >molecules compared to a single molecule representing only a fraction of the > >unit cell? > > No, it would not be more informative: a model in space group X can easily be > expanded to P1. > > JPK > > > Cheers, > Quyen > > On Jan 29, 2016, at 12:18 PM, Keller, Jacob <kell...@janelia.hhmi.org> wrote: > > >Sure, but wouldn’t the same could be achieved by NCS averaging? > > Yes, with complete “NCS” constraints it would be the same. But why do P1 if > so—you’d have all the same issues when deciding which parts of the “NCS” to > constrain (it would be tantamount to SG determination.) Using unmerged data, > however, would have some advantages (one could model the variations between > reflections in a more direct way.) > > I guess the final goal would be to reproduce as accurately as possible the > diffraction images. Thus, crystallographic refinement becomes data-faking (I > guess all science is this same data-faking, in a way.) > > JPK > > > > Ed, regarding the fractional problem with molecular replacement and data to > parameter ratio problem in refinement, I am sure that you know how to get > around these problems ;) > > Quyen > > On Jan 29, 2016, at 10:41 AM, Bernie <b...@uic.edu> wrote: > > Precision is always better when averaging is applied. Mirror planes and > rotations will be perfect rather than exact within experimental error. There > are also singularities in the refinement process that can force the structure > to be symmetrically imperfect. > > Sent from my iPhone > > On Jan 29, 2016, at 8:10 AM, Quyen Hoang <qqho...@gmail.com> wrote: > > Given enough data and modern computing powers, why don’t we just use P1? > > Quyen > > On Jan 29, 2016, at 8:45 AM, George Sheldrick <gshe...@shelx.uni-ac.gwdg.de> > wrote: > > The collection and scaling requires the Laue group but not the space group. > For small molecule structure determination, many more space groups have to be > considered and the choice may be ambiguous (like I222 and I212121) or > difficult, so my current small molecule structure solution program SHELXT > only uses the input space group to deduce the Laue group. After solving the > structure with the data expanded to P1 it uses the phasesto determine the > space group and origin shift. In practice this is much more reliable than > using systematic absences. This was not my idea (see papers by Giacovazzo and > Palatinus), I just wrote a little program to implement it. How the user has > chosen a, b and c is irrelevant, the program outputs the solution in the > conventional setting for the space group in question (as the correct > enantiomorph based on the Friedel differences where appropriate). It also > finds the most compact arrangement of atoms and centers it is the unit-cell. > > Whether this was worth the effort is debatable. SHELXT has been freely > available for the last couple of years, but the open access paper that > explains how it works (Acta A71 (2015) 3-8) is rarely cited. > > George > > > On 01/29/2016 01:06 PM, Ian Tickle wrote: > > Hi Kay > > You are seriously misrepresenting how this works in practice. Isomorphism > always takes precedence over convention: convention is not an absolute > requirement! Convention is the _default_ in the absence of all other > criteria (that's why we have conventions!). Only the _first_ crystal in an > isomorphous series would be indexed by convention, the others would be > indexed using that as a reference (i.e. based on the intensity correlation, > _not_ the unit cell or the assumed space group which may not be reliable, > using REFINDEX, which is what we have always used, or POINTLESS) - very > simple! At Astex we have be doing this for our large fragment screens for 15 > years with no problem. > > In any case we find that assignment of screw axes by axial reflexions is very > unreliable (we have been stung on several occasions!) and we always postpone > choice of space group until _after_ the experimental phasing or MR step, or > even after the structure refinement step, i.e. doing MR and/or refinement in > _all_ 8 possible space groups. So space groups #16, 17, 18 & 19 would always > be initally assigned as space group #16 (P222): that's what XDS does anyway, > so no change there! I would _always_ recommend that procedure over relying > on the axial reflexions for space-group assigment. For some datasets many of > the reflexions on one of the axes were not even measured! (i.e. where the > crystal happens to be aligned along an axis and only a single scan is done). > > Contrary to what you are asserting, the convention you propose has been the > source of great confusion & muddle in the past, whereas the > internationally-agreed one is very clear and has been largely free from > confusion (obviously because it was very carefully designed to be that way). > What happened on a number of occasions in the past (and quite possibly still > happens in some labs) was that the space group was initally assigned as P222 > according to the clear procedure described above, with the conventional cell > correctly assigned as a <= b <= c. What should happen then is that once the > correct space group has been decided, the space group in the header is > changed to that - simple, end of story. However some people think they have > to re-index to the 'standard setting' for SGs 17 & 18 (note that the standard > setting has nothing to do with the conventional cell defined in ITC). So > they end up with files indexed differently - a recipe for disaster, since > they can easily forget to also transform the co-ordinate file from the MR > step, or they do manage to transform it but then mix up the files, thus > R-value = random! I have had to sort out peoples' mess on a number of > occasions which is why I specified the above idiot-proof procedure when we > designed the Astex fragment-screening pipeline back in 2000. > > See these papers by Alan Mighell at NIST (one of the original authors of the > conventional cell tables in ITC) for why we need conventions. > > http://nvlpubs.nist.gov/nistpubs/jres/106/6/j66mig.pdf > http://nvlpubs.nist.gov/nistpubs/jres/107/4/j74mig.pdf > > The most important feature of an international convention is that it is > documented in detail, otherwise how on earth will anyone know how to apply > the convention? The document for the IUCr conventional cells is the ITC, > based in part on the proposals in the above papers. I'm not aware of any > documentation (for all 230 space groups BTW!) for the convention that you are > proposing. I just don't understand why after we've all agreed on a > convention (or at least our national representatives on the relevant IUCr > committees on conventions have on our behalf), why you then want to go and do > something completely different? > > Cheers > > -- Ian > > > > On 29 January 2016 at 09:30, Kay Diederichs <kay.diederi...@uni-konstanz.de> > wrote: > Good morning Graeme, > > as may be obvious from earlier conversations about this, I have a rather > strong opinion about this: even in 2016, > - the a < b < c ordering has no scientific advantage in any way; it may > appear more aesthetic to some > - the ordering has a clear disadvantage if two cell edges are about the same > length, because then, for different measurements, you may end up with > different symmetries. This would be even worse if all three a,b,c are > approximately the same. What a nightmare e.g. in serial crystallography! > > Crystallography is difficult enough. Our choices should be such that we make > it easier for novices to understand it, and to avoid errors. Failure to find > (or think about) the proper re-indexing is one of the most often occurring > problems. > > best, > > Kay > > > > On Fri, 29 Jan 2016 09:13:16 +0000, Graeme Winter > <graeme.win...@diamond.ac.uk> wrote: > > >Good morning all, > > > >It is with some trepidation I raise the following question: does anyone > >still care about reindexing orthorhombic lattices so that the unique axis is > >C? I.e. P21221 => P21212 > > > >Back in the day certain programs would express unhappiness if you fed them > >P21 2 21 (say) data - I am certain that this problem has gone away. Is there > >any reason in 2016 that (say) xia2 should write out symmetry based not cell > >based data? I am leaning towards indexing these so that a < b < c and then > >the screw axes are whatever they are. > > > >How do people feel about this? > > > >Thanks & best wishes Graeme > > > >-- > >This e-mail and any attachments may contain confidential, copyright and or > >privileged material, and are for the use of the intended addressee only. If > >you are not the intended addressee or an authorised recipient of the > >addressee please notify us of receipt by returning the e-mail and do not > >use, copy, retain, distribute or disclose the information in or attached to > >the e-mail. > >Any opinions expressed within this e-mail are those of the individual and > >not necessarily of Diamond Light Source Ltd. > >Diamond Light Source Ltd. cannot guarantee that this e-mail or any > >attachments are free from viruses and we cannot accept liability for any > >damage which you may sustain as a result of software viruses which may be > >transmitted in or with the message. > >Diamond Light Source Limited (company no. 4375679). Registered in England > >and Wales with its registered office at Diamond House, Harwell Science and > >Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-33021 or -33068 > Fax. +49-551-39-22582 > > > - Leonard Chavas - Synchrotron SOLEIL Proxima-I L'Orme des Merisiers Saint-Aubin - BP 48 91192 Gif-sur-Yvette Cedex France - Phone: +33 169 359 746 Mobile: +33 644 321 614 E-mail: leonard.cha...@synchrotron-soleil.fr -
