Dear Gergely, you can concatenate (mm)CIF files, without violating the grammar. Thus, if you want to deposit multiple models at once, just run 'cat 1.mmcif 2.mmcif 3.mmcif > allmy.mmcif' for deposition. This works for CIF, and is accepted e.g. by the IUCR journals.
Best, Tim On Mon, 31 May 2021 17:53:46 +0000 Gergely Katona <gergely.kat...@gu.se> wrote: > Dear Ethan, > > Thank you for your comments! I started a new thread, it was > unfortunate that I brought this up in a discussion about B-factors. I > really wanted to discuss something that is model agnostic and how to > represent uncertainty by sampling. I consider an ensemble model with > multiple partial occupancy molecules is still one model. > > I am not sure if it is possible to use MODEL-ENDMDL loops in pdb or > mmcif format for storing multiple crystallographic models. I assume > it is already possible to store multiple structure factor files (for > refinement, for phasing, different crystals etc) under the same > entry. In my mind, it would be a small step to associate different > data sets distinguished by crystal ID or data block with a particular > model number, but maybe it is not that simple. > > I do not want to create multiple pdb entries just to provide evidence > for the robustness/reproducibility of crystals and crystallographic > models. I would rather use different pdb entries for different > sampling intentions: for example entry 1 contains all the control > crystals, entry 2 contains all the crystals subjected to treatment A, > etc. These would otherwise share identical data reduction and > refinement protocols and most of the metadata. I am afraid I do know > how the PDB and associated services work internally, but I hope > someone here can provide guidance. > > Best wishes, > > Gergely > > > Gergely Katona, Professor, Chairman of the Chemistry Program Council > Department of Chemistry and Molecular Biology, University of > Gothenburg Box 462, 40530 Göteborg, Sweden > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > Web: http://katonalab.eu, Email: gergely.kat...@gu.se > > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Ethan > A Merritt Sent: 29 May, 2021 19:16 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS > > On Saturday, 29 May 2021 02:12:16 PDT Gergely Katona wrote: > [...snip...] > I think the assumption of independent variations per atoms is too > strong in many cases and does not give an accurate picture of > uncertainty. [...snip...] > > > Gergely, you are revisiting a line of thought that historically led > to the introduction of more global treatments of atomic displacement. > These have distinct statistical and interpretational advantages. > > Several approaches have been tried over the past 40 years or so. > The one that has proved most successful is the use of TLS > (Translation/Libration/Screw) models of bulk displacement to > supplement or replace per-atom descriptions. As you say, a per-atom > treatment is often too strong and is not statistically justified by > the experimental data. I explored this with specific examples in > > "To B or not to B?" [Acta Cryst. 2012, D68, 468-477] > http://skuld.bmsc.washington.edu/~tlsmd/references.html > > An NMR-style approach that constructs and refines multiple discrete > models has been been re-invented several times. These treatments are > generally called "ensemble models". IMHO they are statistically > unjustified and strictly worse than treatments based on higher level > descriptions such as TLS or normal-mode analysis. X-ray data is > qualitatively different from NMR data, and optimal treatment of > uncertainty must take this into account. > > best regards > > Ethan > > > > Hi, > > > > It is enough to have Ų as unit to express uncertainty in 3D, but > > one can express it with a single number only in a very specific > > case when the atom is isotropic. Few atoms have a naturally > > isotropic distribution around their mean position in very high > > resolution protein crystal structures. The anisotropic atoms can be > > described by a 3x3 matrix, where each row and column is associated > > with the uncertainty in a specific spatial direction. The matrix > > elements are the product of the uncertainty in these directions. > > The diagonal elements will be the square of uncertainty in the same > > direction and they should be always positive, the off-diagonal > > combination of directions are covariances (+,0 or -). In the end, > > every element will have a unit distance*distance and the matrix > > will be symmetric. We cannot just take the square root of the > > matrix elements and expect something meaningful, if for no other > > reason the problem with negative covariances. To calculate the > > square root on the matrix itself one has to diagonalize it first. > > The height of a person in your example sounds easy to define, but > > the mathematical formalism will not decide that for me. I can also > > define height as the longest cord of a person or the maximum > > elevation of a car mechanic under a car. Through diagonalization > > one can at least extract some interesting, intuitive, principal > > directions. The final product, the sqrt(matrix), is not more > > intuitive to me. To convert it to something intuitive I would have > > to diagonalize square rooted matrix again. So shall we make an > > exception for the special, isotropic description? Or use general > > principles for isotropic and anisotropic treatments? > > > > About what B-factors are, I like to think about them as necessary > > model parameters. Computational biologists also use them for > > benchmarking their molecular dynamics models. They are also > > reproducible to the extent that one can identify specific atoms > > just based on their anisotropic tensor from independent structure > > determinations in the same crystal form. They are of course not > > immune to errors and variation. > > > > I also wonder how we can represent model parameter variation in the > > best way. I admire NMR spectroscopists’ approach to deposit > > multiple samples from a structural distribution. One could > > reproduce their conclusions without assuming any sort of error > > model from these samples. In crystallography, we have more and more > > distributions to deal with because we are swimming in data. It is > > easy to sample/resample data sets from the same or different > > crystals (SFX for example). Which can lead to many replicates of > > structural models. I cannot really motivate to create multiple PDB > > entries for these replicates, it is not good for to reader to try > > to understand which PDB codes belong to which group of samples. > > Maybe it works for up to 10 structures, but how about a 100? Is it > > possible to deposit crystal structures as a chain of model/data > > pairs under the same entry? It is possible to just make a tarball > > and deposit in alternative services such as Zenodo, but it would be > > a pity to completely bypass the PDB. I can think of more compact > > description of structural distributions, for example mean positions > > and mean B-factors of atoms with their associated covariance > > matrices, analogously how MD trajectories can be described as > > average structures and covariance matrices. I think the assumption > > of independent variations per atoms is too strong in many cases and > > does not give an accurate picture of uncertainty. > > > > Best wishes, > > > > Gergely > > > > Gergely Katona, Professor, Chairman of the Chemistry Program > > Council Department of Chemistry and Molecular Biology, University > > of Gothenburg Box 462, 40530 Göteborg, Sweden > > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > > Web: http://katonalab.eu, Email: gergely.kat...@gu.se > > > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of > > Hughes, Jonathan > > Sent: 28 May, 2021 14:49 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS > > > > hi ian, > > yes, that aspect was in my mind, a bit, but i wanted to keep it > > simple. my point wasn't really how the "uncertainty" parameter is > > derived but rather its units. i can imagine that uncertainty in 3D > > could be expressed in ų (without helping the naïve user much) or > > in Å (which to me at least seems useful), but Ų (i.e. the B > > factor) seems neither logical nor helpful in this context, > > irrespective of its utility elsewhere. if you just see the B factor > > as a number, ok, you can do the √ in your head, but if it's > > visualized as in pymol/putty larger uncertainties become > > exaggerated – which is another word for "misrepresented". cheers j > > > > Von: Ian Tickle <ianj...@gmail.com<mailto:ianj...@gmail.com>> > > Gesendet: Freitag, 28. Mai 2021 12:10 > > An: Hughes, Jonathan > > <jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-gie > > ssen.de>> > > Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > > Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS > > > > > > Hi Jonathan > > > > On Thu, 27 May 2021 at 18:34, Hughes, Jonathan > > <jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-giessen.de>> > > wrote: > > > > "B = 8π2<u2> where u is the r.m.s. displacement of a scattering > > center, and <...> denotes time averaging" > > > > Neither of those statements is necessarily correct: u is the > > _instantaneous_ displacement which of course is constantly changing > > (on a timescale of the order of femtoseconds) and cannot be > > measured. So u2 is the squared instantaneous displacement, <u2> > > is the mean-squared displacement, and so the root-mean-squared > > displacement (which of course is amenable to measurement) is > > sqrt(<u2>), not the same thing at all as u. > > > > Incidentally, the 8π2 constant factor comes from > > Fourier-transforming the Debye-Waller factor expression I mentioned > > earlier. > > > > Also for crystals at least, the averaging is not only over time, > > it's over all unit cells, i.e. the displacements are not only > > thermal in origin but also due to spatial static disorder > > (instantaneous differences between unit cells). > > > > > > it would seem to me that we would be able to interpret things MUCH > > more easily with u rather than anything derived from u². So then I > > think what you mean is sqrt(<u2>) rather than <u2>, which seems not > > unreasonable. > > > > Cheers > > > > -- Ian > > > > > > > > > > > > ________________________________ > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ###################################################################### > > ## > > > > 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/ > > > > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > ######################################################################## > > 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/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## 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/
pgpUzjiG7nbn2.pgp
Description: OpenPGP digital signature
