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ns with high precision but the probabilities the u net assigns for a hole also appear to be suitable measures for the collectability of a hole altogether ptolemy provides an all in one solution for reliable and accurate automatic targeting of squares and holes on single particle cryo em grids this is a big step towards the full automation of cryo em screening and data collection and is readily implemented in the microscope operation software leginon for details of the implementation see cheng et al 2023 also published in this issue of iucrj while ptolemy uses specifically tailored and tuned cnn and u net machine learning approaches to achieve high accuracy for recognizing and ranking squares and holes other software have approached the problem of automatic data acquisition in slightly different ways a conceptually similar approach was taken by smartscope bouvette et al 2022 which utilized dedicated square and hole finders to select targets for the operator in comparison to ptolemy the smartscope square and hole recognition procedures are based on an r cnn with resnet50 architecture and a yolov5 model with cspnet backbone for square and hole recognition respectively it remains to be seen which deep learning implementation yields better performance in real life cryoem imaging sessions notably smartscope implemented ptolemy as an alternative to their own square and hole recognition algorithms bouvette viverette 2022 so direct comparison will be possible a conceptually different approach is taken by cryorl li et al 2022 instead of attempting to generate a complete selection of suitable squares and holes prior to cryo em imaging cryorl treats the selection of imaging targets as a path planning problem where the algorithm is rewarded when imaging good targets currently a target is considered good when it yields a cryo em image with high information content which inversely correlates with ice layer thickness however the thinnest ice layer possible might not be a suitable target for acquiring data of sensitive or very large protein complexes d imprima et al 2019 noble et al 2018 instead other results from on the fly data analysis like complex integrity particle number per image or the orientation distribution of particle views in the 3d reconstructions could represent suitable quality targets it seems likely that combining the approaches taken by ptolemy smartscope and cryorl will lead to very powerful automatic cryo em data acquisition tools such tools would first generate highly accurate initial collectability rankings of squares and holes whereas the process of data collection would be guided by sample specific on the fly decision making that is based on data analysis results acknowledgements the author thanks rebecca thompson and james walshe for critical reading of the manuscript references bouvette j huang q riccio a a copeland w c bartesaghi a borgnia m j 2022 elife 11 e80047 bouvette j viverette e 2022 external plugin installation smartscope documentation https docs smartscope org docs v0 7 carragher b kisseberth n kriegman d milligan r a potter c s pulokas j reilein a 2000 j struct biol 132 33 45 cheng a kim p t kuang h mendez j h chua e y d maruthi k wei h sawh a aragon m f serbynovskyi v neselu k eng e t potter c s carragher b bepler t noble a j 2023 iucrj 10 77 89 dhillon a verma g k 2020 artif intell 9 85 112 d imprima e floris d joppe m sánchez r grininger m kühlbrandt w 2019 elife 8 e42747 grant t rohou a grigorieff n 2018 elife 7 e35383 kim p t noble a j cheng a bepler t 2023 iucrj 10 90 102 kühlbrandt w 2014 science 343 1443 1444 li y fan q cohn j demers v lee j y yip l cianfrocco m a vos s m 2022 biorxiv 2022 06 17 496614 mastronarde d n 2005 j struct biol 152 36 51 mcmullan g faruqi a r henderson r 2016 methods enzymol 579 1 17 noble a j dandey v p wei h brasch j chase j acharya p tan y z zhang z kim l y scapin g rapp m eng e t rice w j cheng a negro c j shapiro l kwong p d jeruzalmi d des georges a potter c s carragher b 2018 elife 7 e34257 nogales e 2016 nat methods 13 24 27 passmore l a russo c j 2016 methods enzymol 579 51 86 punjani a rubinstein j l fleet d j brubaker m a 2017 nat methods 14 290 296 ronneberger o fischer p brox t 2015 arxiv 150504597 scheres s h w 2012 j struct biol 180 519 530 sigworth f j 2016 microscopy oxf 65 57 67 tegunov d cramer p 2019 nat methods 16 1146 1152 thompson r f iadanza m g hesketh e l rawson s ranson n a 2019 nat protoc 14 100 118 weissenberger g henderikx r j m peters p j 2021 nat methods 18 463 471 this article was originally published in iucrj 2023 10 4 5 read less commentary optimizing disordered crystal structures read more optimizing disordered crystal structures anthony linden disordered crystal structures constitute about 28 of the entries in the cambridge structural database groom et al 2016 it is always exciting when a new data set comes off the diffractometer and one hopes for a rapid refinement of what is expected to be a routine structure determination but then the discovery of disorder ruins one s day when one realises that considerable time and effort will be needed to arrive at an optimal structure model sometimes the disorder is only present in a solvent molecule or counterion e g a tumbling pf 6 anion where it is not so critical to develop a perfect model but nonetheless every improvement in the disorder model for such species usually improves the agreement factors and the precision of the atomic coordinates for all components in the structure thereby leading to more precise geometric parameters even in the non disordered main component for many analyses the geometric parameters are the most tangible results of interest so obtaining their best precision is important in crystal structures where the molecule or fragment of interest is disordered the disorder might have no consequences for the understanding of the chemical species present such as conformational variations in the puckering of a five membered ring or in the orientation of a terminal cf 3 group in such cases modelling the disorder is often but not always relatively straightforward at the other extreme the challenge of dealing with extensive subtle or even full molecule disorder often requires much effort because the positions of many atoms from the various disorder components are almost overlapping and it can be tricky to set up the best combination of restraints and or constraints to allow the refinement to work smoothly while maintaining the correct chemical and geometrical logic of the species present full molecule disorder can occur when the topology and polarity of the compound is such that the molecule can slot into its space in the crystal structure without caring about which way around it sits a similar scenario can occur when more than one chemical species with similar topology is present in the crystal and they occupy the same crystallographic site a mixture of diastereoisomers is one such example of course these topological considerations are not necessarily limited to entire molecular species whether it is a molecular or an extended structure a part of the asymmetric unit such as a single ligand might also fit into its cavity in more than one orientation or conformation a mixed crystal full molecule disorder situation is described in this issue of acta crystallographica section c by parkin et al 2023 the authors revisit the product of an organic reaction published by some of the same authors mohamed et al 2016 which at the time was described as the meso isomer of e e 1 10 1 2 bis 4 chlorophenyl ethane1 2 diyl bis phenyldiazene disordered across a crystallographic centre of inversion some unusual geometry subsequently noticed in the original model prompted the reevaluation the new interpretation of the data leads to the conclusion that the crystal structure is more likely to be a three component superposition of the meso form with additionally the s s and r r enantiomers such a superposition is feasible given the spatial similarities of the isomers the matter is made more complicated by the question of whether or not the true space group is cc or the centrosymmetric c 2 c while the motivation of parkin et al 2023 is to improve on the original interpretation of the structure the means of getting there is presented in a clear and instructive way the article is thus a good learning example for dealing with a highly disordered structure and for what some people call forensic crystallography not only do the authors contend with modelling the disorder but also deduce which chemical compounds are most likely to be present and address the space group ambiguities usually this sort of problem requires many trial refinements and in general practitioners should not feel reluctant to try out various ideas before settling on their final model the problem is approached from both crystallographic and chemistry points of view that is the models for each of the disordered components have to be geometrically logical as it is unlikely that such organic molecules would be geometrically distorted the models should also account for the observed electron density distribution the presence of cl atoms in these molecules makes their disordered positions stand out more clearly thereby giving a starting point for developing the models which understandably require a significant array of restraints and constraints as with many complex disorder problems there is probably not a unique way to select restraints and constraints to arrive at an acceptable model the authors themselves state it is unlikely that any two crystallographers would settle on the same combination of constraints restraints finally the chemical origin of the enantiomers and meso isomer has to be understood originally only the presence of the meso compound had been assumed this highlights the importance of critical and logical thinking and a good dialogue between the crystallographer and the scientist s producing the substances and interpreting the other spectroscopic data if they are not the same person these comments are not intended as a criticism of the original work sometimes another pair of eyes and a different viewpoint reveal things that the others have not noticed coincidentally this issue of the journal reports another disordered mixed crystal structure where the disorder is a consequence of the superposition of two diastereoisomers one of which is additionally conformationally disordered at the same crystallographic site in the crystal treatment of which requires a three component disorder model although full molecule disorder is probably not present linden et al 2023 anecdotally i was recently contacted by a young crystallographer who was struggling with the interpretation of a disordered structure that looked somewhat like the expected synthesis product but was strange in other respects especially some excessively long bonds after discussing the synthesis of the material we concluded that the crystal was a mixed crystal composed of unreacted starting material and product and the two species had crystallized randomly at the same crystallographic site it was then possible to develop an appropriate disorder model for the structure albeit still with some non ideal geometry i suggested that if it was at all possible still some additional attempts at carefully optimizing the reaction and or work up and separation procedures might allow one to obtain the product in a more pure form indeed the desired pure product was obtained subsequently and a clean crystal structure ensued thus obviating the need to continue with or attempt to publish the mixed crystal structure of course the separation or purification of mixtures can sometimes be extremely difficult but if tweaks to the procedures have not yet been tested further attempts might be more fruitful than trying to continue with a messy inferior quality or even ambiguous mixed crystal structure determination small molecule crystallographers are fortunate today to have some excellent tools available to assist with the modelling of disorder while the program shelxl sheldrick 2015 has long had an extensive array of restraint and constraint instructions sadi same dfix dang simu delu and rigu to name just a few manually developing the initial disorder model was sometimes cumbersome nowadays the olex 2 software dolomanov et al 2009 as one example has excellent and clever tools in the graphical user interface gui which allow one after a little practice to split drag and rotate fragments conveniently in order to obtain a good starting approximation to the disorder and then apply the appropriate restraints and or constraints the gui of shelxle hübschle et al 2011 can be used in a similar way olex 2 also has a fragment database which can be used to help model common fragments or solvent molecules excellent youtube tutorials demonstrating many of the features of both of these programs not just disorder handling are available online further discourses on many aspects of obtaining the best results from a crystal structure determination including the handling disordered structures can be found in vinaya et al 2023 clegg 2019 and linden 2020 references clegg w 2019 acta cryst e 75 1812 1819 dolomanov o v bourhis l j gildea r j howard j a k puschmann h 2009 j appl cryst 42 339 341 groom c r bruno i j lightfoot m p ward s c 2016 acta cryst b 72 171 179 hübschle c b sheldrick g m dittrich b 2011 j appl cryst 44 1281 1284 linden a 2020 acta cryst e 76 765 775 linden a bucher c b gubler r villalgordo j m heimgartner h 2023 acta cryst c 79 104 111 mohamed s k younes s h h abdel raheem e m m horton p n akkurt m glidewell c 2016 acta cryst c 72 57 62 parkin s glidewell c horton p n 2023 acta cryst c 79 77 82 sheldrick g m 2015 acta cryst c 71 3 8 vinaya basavaraju y b srinivasa g r shreenivas m t yathirajan h s parkin s 2023 acta cryst e 79 54 59 this article was originally published in acta cryst 2023 c 79 69 70 read less obituary olga kennard obe frs 1924 2023 read more olga kennard obe frs 1924 2023 michael francis dr olga kennard giving opening remarks at the csd s 50th anniversary celebration from the ccdc it is with great sadness that we learn of the passing of dr olga kennard her long successful life was full of many achievements including founding the cambridge structural database csd which is now a fundamental resource that supports the global development of new drugs and materials that benefit us all is used in chemistry education and contributes to the advancement of science in this obituary for dr kennard we celebrate and recognize her many achievements in the scientific community born in hungary dr kennard moved to the uk in 1939 just before the outbreak of the second world war after graduating from the university of cambridge in 1944 she joined the cavendish laboratory under lawrence bragg as an assistant to max perutz in the department of physics after completing the first 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