June 2018 - phenixbb - phenix-online.org

Fwd: phenixbb post from [email protected]
by Nigel Moriarty 04 Jun '18

04 Jun '18

Folks There was a post from Gerard Bricogne that was lost (as far as I can see) in the internals of MailMan because of a 40Kb size limit and other reasons unknown. It was posted to the CCP4BB so you may have already seen it. Please find it below. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov Subject: Table 1 successor in 3D? Dear all, Bernhard Rupp has just published a "Perspective" article in Structure, accessible in electronic form at https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 in which part of his general argument revolves around an example (given as Figure 1) that he produced by means of the STARANISO server at http://staraniso.globalphasing.org/ . The complete results of his submission to the server have been saved and may be accessed at http://staraniso.globalphasing.org/Gallery/Perspective01.html and it is to these results that I would like to add some annotations and comments. To help with this, I invite the reader to connect to this URL, type "+" a couple of times to make the dots bigger, and press/toggle "h" whenever detailed information on the display, or selection of some elements, or the thresholds used for colour coding the displays, needs to be consulted. The main comment is that the WebGL interactive 3D display does give information that makes visible characteristics that could hardly be inferred from the very condensed information given in Table 1, and the annotations will be in the form of a walk through the main elements of this display. For instance the left-most graphical object (a static view of which is attached as "Redundancy.png") shows the 3D distribution of the redundancy (or multiplicity) of measurements. The view chosen for the attached picture shows a strong non-uniformity in this redundancy, with the region dominated by cyan/magenta/white having about twice the redundancy (in the 6/7/8 range) of that which prevails in the region dominated by green/yellow (in the 3/5 range). Clear concentric gashes in both regions, with decreased redundancy, show the effects of the inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline. The blue spherical cap along the a* axis corresponds to HKLs for which no measurement is available: it is clearly created by the detector being too far from the crystal. The second (central) graphical object, of which a view is given in Figure 1 of Bernhard's article and another in the attached picture "Local_I_over_sigI.png") shows vividly the blue cap of measurements that were missed but would probably have been significant (had they been measured) cutting into the green region, where the local average of I/sig(I) ranges between 16 and 29! If the detector had been placed closer, significant data extending to perhaps 3.0A resolution would arguably have been measured from this sample. The right-most graphical object (of which a static view is attached as "Debye-Waller.png") depicts the distribution of the anisotropic Debye-Waller factor (an anisotropic generalisation of the Wilson B) of the dataset, giving yet another visual hint that good data were truncated by the edges of a detector placed too far. Apologies for such a long "STARANISO 101" tutorial but Bernhard's invitation to lift our eyes from the terse numbers in Table 1 towards 3D illustrations of data quality criteria was irresistible ;-) . His viewpoint also agrees with one of the main purposes of our STARANISO developments (beyond the analysis and remediation of anisotropy, about which one can - and probably will - argue endlessly) namely contribute to facilitating a more direct and vivid perception by users of the quality of their data (or lack of it) and to nurturing evidence-based motivation to make whatever extra effort it takes to improve that quality. In this case, the undeniable evidence of non-uniformity of redundancy and of a detector placed too far would give immediate practical guidance towards doing a better experiment, while statistics in Table 1 for the same dataset would probably not ... . Thank you Bernhard! With best wishes, Gerard, for and on behalf of the STARANISO developers

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d99 beyond Nyquist?
by Ricardo Righetto 03 Jun '18

03 Jun '18

Hi, I've seen the d99 criterion in phenix.mtriage reporting a resolution value beyond Nyquist (=2.0 A), or very close to Nyquist in another case. For these particular maps, which are from the same dataset processed with two different single-particle analysis packages (internal benchmarking), half-map FSC-based methods (including blocres) report resolutions in the range of 3.0-3.5 A which are consistent with the features I can see. How can I interpret this? I understand that d99 starts omitting Fourier samples from the corners of the reciprocal box, but does it make sense to report a value beyond Nyquist? I tried supplying unfiltered, masked and unmasked versions of the maps with barely any variation in the d99 results. Thanks in advance for helping figuring this out! Best wishes, -- Ricardo Diogo Righetto

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 01 Jun '18

01 Jun '18

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2018 issue is 22 June 2018. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Table 1 successor in 3D?
by Gerard Bricogne 01 Jun '18

01 Jun '18

Dear all, Bernhard Rupp has just published a "Perspective" article in Structure, accessible in electronic form at https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 in which part of his general argument revolves around an example (given as Figure 1) that he produced by means of the STARANISO server at http://staraniso.globalphasing.org/ . The complete results of his submission to the server have been saved and may be accessed at http://staraniso.globalphasing.org/Gallery/Perspective01.html and it is to these results that I would like to add some annotations and comments. To help with this, I invite the reader to connect to this URL, type "+" a couple of times to make the dots bigger, and press/toggle "h" whenever detailed information on the display, or selection of some elements, or the thresholds used for colour coding the displays, needs to be consulted. The main comment is that the WebGL interactive 3D display does give information that makes visible characteristics that could hardly be inferred from the very condensed information given in Table 1, and the annotations will be in the form of a walk through the main elements of this display. For instance the left-most graphical object (a static view of which is attached as "Redundancy.png") shows the 3D distribution of the redundancy (or multiplicity) of measurements. The view chosen for the attached picture shows a strong non-uniformity in this redundancy, with the region dominated by cyan/magenta/white having about twice the redundancy (in the 6/7/8 range) of that which prevails in the region dominated by green/yellow (in the 3/5 range). Clear concentric gashes in both regions, with decreased redundancy, show the effects of the inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline. The blue spherical cap along the a* axis corresponds to HKLs for which no measurement is available: it is clearly created by the detector being too far from the crystal. The second (central) graphical object, of which a view is given in Figure 1 of Bernhard's article and another in the attached picture "Local_I_over_sigI.png") shows vividly the blue cap of measurements that were missed but would probably have been significant (had they been measured) cutting into the green region, where the local average of I/sig(I) ranges between 16 and 29! If the detector had been placed closer, significant data extending to perhaps 3.0A resolution would arguably have been measured from this sample. The right-most graphical object (of which a static view is attached as "Debye-Waller.png") depicts the distribution of the anisotropic Debye-Waller factor (an anisotropic generalisation of the Wilson B) of the dataset, giving yet another visual hint that good data were truncated by the edges of a detector placed too far. Apologies for such a long "STARANISO 101" tutorial but Bernhard's invitation to lift our eyes from the terse numbers in Table 1 towards 3D illustrations of data quality criteria was irresistible ;-) . His viewpoint also agrees with one of the main purposes of our STARANISO developments (beyond the analysis and remediation of anisotropy, about which one can - and probably will - argue endlessly) namely contribute to facilitating a more direct and vivid perception by users of the quality of their data (or lack of it) and to nurturing evidence-based motivation to make whatever extra effort it takes to improve that quality. In this case, the undeniable evidence of non-uniformity of redundancy and of a detector placed too far would give immediate practical guidance towards doing a better experiment, while statistics in Table 1 for the same dataset would probably not ... . Thank you Bernhard! With best wishes, Gerard, for and on behalf of the STARANISO developers

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