Dear Quyen,
It seems that you have an assumption that there is something special about the P1 spacegroup that means that the contents are more biologically relevant than in any other spacegroup. This just isn't the case- you will have just as relevant or non-relevant oligomers in P1 as in any other spacegroup (I am dealing with this now - for the same structure I have at least 3 different spacegroups, including P1, and there is one single tetramer and two dimers in the P1 case; the structure in solution is a tetramer which can be seen in multiple ways and the other spacegroups have the tetramer, but one uses crystallographic symmetry to see it).
cheers, tom
Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
[log in to unmask]
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Quyen Hoang [[log in to unmask]]
Sent: Saturday, January 30, 2016 11:30 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Spacegroups, screw axes and ordering
Indeed that's the assumption that I accept, but only because I have to. If I could solve the unit cells independently I would because doing so would resolve static disorders and alternative conformations.
Quyen
Sent from my BlackBerry 10 smartphone.
Original Message
From: Ronald E Stenkamp
Sent: Friday, January 29, 2016 7:23 PM
To: Quyen Hoang
Cc: [log in to unmask]
Subject: Re: [ccp4bb] Spacegroups, screw axes and ordering
This may be a diversion from your main point, but I have questions about solving all structures in P1.
Isn't it true that by refining your structure in P1, you're accepting the assumption that the crystal is built up of a collection of identical unit cells related by translational symmetry?
If that's an acceptable assumption, why then is it not acceptable to believe other symmetry operations (screws, rotations, etc) should also be included in your model of the crystal structure?
If you want to refine everything in P1 and then test for whether there's additional symmetry in your model, why not carry out the same testing for the unit cell assumption? (I know why I wouldn't do that, i.e., not enough experimental data or computer time to model the structure of 10**18 molecules). But maybe you could reindex your data set in a larger unit cell, and then look at the model to see if the translational symmetry holds or not? Of course, if the additional reflections all have intensities of zero, the resulting model will show the translational symmetry.
Ron Stenkamp
On Fri, 29 Jan 2016, Quyen Hoang wrote:
> Hmm...really?
> Imagine a scenario where you built a structure consisting of a residue with a sidechain existing in two conformations (buýilt as alternative
> conformations with 0.5 occupancy) and upon expanding to P1 you find each monomer having a full occupancy of each conformation. I have not seen
> one, but would not it be a possibility?
>
> I am not advocating for changing the way things are done, and I don't want it to change either. Just curious how people feel because I like to
> look at my models in P1 when possible (not just symmetry generated).
>
> Quyen
>
> Quyen
>
> Sent from my BlackBerry 10 smartphone.
> From: Ethan A Merritt
> Sent: Friday, January 29, 2016 5:36 PM
> To: Quyen Hoang
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] Spacegroups, screw axes and ordering
>
> On Friday, 29 January, 2016 16:46:35 Quyen Hoang wrote:
>
> > Let get back to science for a moment, assuming that there is enough data (as stated in my original post about this) would you not agree that
> the models build into a P1 space group would represent the content of the unit cell more accurately than a higher space group (albeit could be
> insignificant)?
>
>
>
> Two possibilities:
>
> 1) No, the models come out identical and therefore the accuracy is the same
>
>
>
> 2) No, the models come out differently, so you have done something wrong.
>
>
>
> If the true symmetry of the crystal is greater than P1 there is nothing
>
> to distinguish one crystallographic symmetry-related molecule from another,
>
> so you cannot gain anything by describing them as two distinct entities [*].
>
>
>
> Ethan
>
>
>
>
>
>
>
> [*] This is assuming we are dealing with non-centrosymmetric crystals.
>
> If there are D- and L- copies of a molecule present then yes they can
>
> be distinguished from each other by handedness. But you still do not
>
> gain anything by treating them separately in model-building or refinement.
>
>
>
>
>
> > After your refinement has converged, don’t you always expand to look at the packing and potential oligomeric states of your molecule? Let's
> say that you have a true tetramer, what would be lost if you report your structural model in P1 instead of P212121?
>
> > I mean, is there a theoretical or scientific reason against reporting P1 for a crystal system consisting of higher symmetry?
>
> >
>
> > Cheers,
>
> > Quyen
>
> >
>
> > > On Jan 29, 2016, at 4:27 PM, CHAVAS Leonard <[log in to unmask]> wrote:
>
> > >
>
> > > Sorry if I don't buy it. Just personal feeling. I don't see how someone capable of navigating through the coordinates, see meaningful
> interactions, highlight those and understand them, would not be able to press these buttons. While some programs indeed do not have these
> options (which makes me wonder about the usefulness of these programs by the way), most of those would. Let me join also Jacob's comment on the
> non usefulness of P1 in here, and send these non-experts either to PISA or to other experts more knowledgeable, say the people who solved these
> structures for instance.
>
> > >
>
> > > Your point on the mtz file is interesting. We are now moving things toward some non-crystallographers in need to install quite a few
> programs, if not at least libraries, and put in these mtz files enough information to reproduce all the non-standard refinement procedures
> experts do apply for their structure refinement. Not to mention 5A structures for which auto build might be trickier to run than building in 1A
> maps.
>
> > >
>
> > > Leo
>
> > >
>
> > >> On 29 Jan 2016, at 22:02, Quyen Hoang <[log in to unmask]> wrote:
>
> > >>
>
> > >> 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.
>
> > >>
>
> > >> Quyen
>
> > >>
>
> > >>> On Jan 29, 2016, at 3:16 PM, CHAVAS Leonard <[log in to unmask]> 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 <[log in to unmask]> 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 PDBý, 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; [log in to unmask]
>
> > >>>> 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 <[log in to unmask]> 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 <[log in to unmask]> 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 <[log in to unmask]> 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 <[log in to unmask]> 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 <[log in to unmask]> 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 <[log in to unmask]> 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
>
> > >>>>>
>
> > >>>>> --
>
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>
> > >>>>
>
> > >>>>
>
> > >>>>
>
> > >>>>
>
> > >>>>
>
> > >>>
>
> > >>> -
>
> > >>> 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: [log in to unmask]
>
> > >>> -
>
> > >>>
>
> > >
>
> > > -
>
> > > 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: [log in to unmask]
>
> > > -
>
> > >
>
> --
>
> Ethan A Merritt
>
> Biomolecular Structure Center, K-428 Health Sciences Bldg
>
> MS 357742, University of Washington, Seattle 98195-7742
>
>
>
>
>
>
|
