Good thoughts, although there are always exceptions. For example, if a crystal contact is mediated by an extended domain that is capable of adopting multiple conformations (due to elbow motion, for example), then it may allow multiple crystal forms. It happens a lot in RNA crystals, but can also be found in protein crystals.
From the user’s point of view, if crystal dehydration leads to space group change, it is a new crystal form. If the refinement does not kick off with routine fiddling of refinement parameters, it is equivalent to a new crystal form, because one has to go through the same procedure as to solve a new crystal form. Ailong > On Dec 9, 2020, at 1:54 AM, Manfred S. Weiss > <[email protected]> wrote: > > Dear James, > > let's spin the thought a bit further. What if there is a new program > (Phaser-II) some day, > for which the coordinates in your "new crystal form" are all of a sudden > within the > radius of convergence again? Does this bring your "new crystal form" > back to the old > crystal form again? > > I'd say it is neither cell dimensions nor space group that define a new > crystal form. It > is the packing of the molecules. It happens quite often in dehydration > experiments > that molecules in a lattice move a bit and symmetry elements are lost or > new symmetry > elements are created. The space group changes, as well as the unit cell > dimensions. But > the packing remains essentially the same. You can usually infer what > happens, but you > still need molecular replacement to actually solve the "new" form. > > Best, Manfred > > > Am 09.12.2020 um 01:56 schrieb James Holton: >> I have a semantics question, and I know how much this forum loves >> discussing semantics. >> >> We've all experienced non-isomorphism, where two crystals, perhaps >> even grown from the same drop, yield different data. Different enough >> so that merging them makes your overall data quality worse. I'd say >> that is a fairly reasonable definition of non-isomorphism? Most of the >> time unit cell changes are telling, but in the end it is the I/sigma >> and resolution limit that we care about the most. >> >> Now, of course, even for non-isomorphous data sets you can usually >> "solve" the non-isomorphous data without actually doing molecular >> replacement. All you usually need to do is run pointless using the >> PDB file from the first crystal as a reference, and it will re-index >> the data to match the model. Then you just do a few cycles of rigid >> body and you're off and running. A nice side-effect of this is that >> all your PDB files will line up when you load them into coot. No >> worries about indexing ambiguities, space group assignment, or origin >> choice. Phaser is a great program, but you don't have to run it on >> everything. >> >> My question is: what about when you DO have to run Phaser to solve >> that other crystal from the same drop? What if the space group is the >> same, the unit cell is kinda-sorta the same, but the coordinates have >> moved enough so as to be outside the radius of convergence of >> rigid-body refinement? Does that qualify as a different "crystal >> form" or different "crystal habit"? Or is it the same form, and just >> really non-isomorphous? >> >> Opinions? >> >> -James Holton >> MAD Scientist >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ > > -- > Dr. Manfred S. Weiss > Macromolecular Crystallography > Helmholtz-Zentrum Berlin > Albert-Einstein-Str. 15 > D-12489 Berlin > Germany > > > ________________________________ > > Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren > e.V. > > Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta > Koch-Unterseher > Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, > Thomas Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
