>No, I wasn’t talking about crystal packing, I was thinking about potential >homo oligomeric interactions that might be important for function. If we are talking about the simplicity of pushing couple buttons and saving disk space and bandwidth, then I guess the same argument could be made that a simple MTZ file containing phases should suffice? The non-crystallographer would simply press a few buttons to generate a model with auto build? But I have a feeling those couple of buttons might not be so obvious to people in other fields.
Maybe just the number "42" would suffice? JPK Quyen > On Jan 29, 2016, at 3:16 PM, CHAVAS Leonard > <[email protected]> wrote: > > 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 <[email protected]> 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; [email protected] >> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> >> 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 <[email protected]> >> 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 >> <[email protected]> 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: [email protected] > - >
