Re: [ccp4bb] which space group?!?

Dear Jürgen, dear Katherine, Sorry for a late reaction. In our article in Acta Cryst., 2009, D65, 1283-1291 (Section 4) we show an accurate distribution of the most frequent R, Rfree, Rfree-R as a practically linear function of the Log(resolution) , and not that of the resolution itself, and

Re: [ccp4bb] difference between polar angle and eulerian angle

Dear Ed, It looks like the problem is not yet closed, so I'll add my remarks. In addition to very detailed comments by Ian, Tim and others, it might be useful to look our article in J.Appl.Cryst (1997), 30, 402-410, which addresses exactly these confusing points: what is rotated, what is

Re: [ccp4bb] crystallographic confusion

Dear Dale, dear Kay, last year, we discussed this kind of problems (Urzhumtseva et al., 2013, Acta Cryst., D69, 1921-1934). Our approach does not tell you where to cut your data and which reflections to accept / reject but as soon as you have your set of reflections, you calculate very

[ccp4bb] effective resolution : programs

and you can try it. With best wishes, Sacha De : Boaz Shaanan [bshaa...@bgu.ac.il] Envoyé : samedi 19 avril 2014 17:28 À : Alexandre OURJOUMTSEV; CCP4BB@JISCMAIL.AC.UK Objet : RE: [ccp4bb] crystallographic confusion ... Have the criteria that you propose

[ccp4bb] GUI program to calculate effective resolution of a data set

Dear All, Recently, there was a ccp4bb conversation concerning the definition of a ‘real’ (effective) resolution of (incomplete) diffraction data sets. I am happy to announce that a corresponding GUI program EFRESOL is available now and you may download it from the Web site:

[ccp4bb] efresol (effective resolution ) : updated version

Dear All, Sorry for spamming. Thanking to the criticism and advices from a number of recent testers (in particular, Mark van Raaij, Oleg Sobolev, Pavel Afonine), we produced an updated version (version 2.3) of the program EFRESOL to calculate the effective and optical resolutions and the

Re: [ccp4bb] Hi - euler angles conversion

Dear Vijay, (sorry, it looks like my previous mail went being unfinished). There is a program developed in purpose for this goal : Urzhumtseva, L.M., Urzhumtsev, A.G. (1997) Tcl/Tk based programs. II. CONVROT: program to recalculate different rotation descriptions. J.Appl. Cryst., 30, 402-410

[ccp4bb] Re : Re: [ccp4bb] How to make fft-map more physically meaningful?

Dear Hailiang,As James said, the hermitian symmetry of Fourier coefficients, F(h)=F*(-h), that is known in diffraction theory as the Friedel's law, is an equivalent of the condition that the corresponding function (electron density) is a real function.I think if you need further information you

[ccp4bb] RE : [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

Dear Ethan, Just answering your last remarks, very many years ago I've done tests (unpublished) where I tried to estimate the magnitudes Fbulk and PHASES Pbulk for the reflections due to bulk solvent. It came out that : - for high-resolution reflections the magnitudes are small (everybody

Re: [ccp4bb] diverging Rcryst and Rfree

Dear Rakesh, dear Artem, Since the initial question is not precise (which kind of comments are expected?) I may mention that the most frequent values of R, Rfree and DeltaR (that is asked about) are given in our work published in 2009 in Acta Cryst., D65, 1283-1291. Interestingly, they are

Re: [ccp4bb] Babinet solvent correction / comment for imperfect models

Dear all, Sorry to come back late, when the discussion is over, with one more remark relevant to the bulk solvent modeling. I've just got a comment by a colleague of mine, Adam Ben-Shem, who kindly agreed that I post his message (below) to CCP4bb. I think he is completely right saying that

Re: [ccp4bb] Citations in supplementary material

Thank you, Victor ! It is my many-years complain, and I tried to point it out orally at a number of conferences many times concerning both the publications and presenting results in posters. Very-very often we see a structure as given with no comments which (often very multiple and

Re: [ccp4bb] Same protein, different molecule numbers per ASU

Dear Ferrol, Could you let us know the unit cell parameters for both these crystals ? (did I miss them somewhere in your previous mails?). I wonder if in fact this is not the same packing with minor variation. Sacha De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de ferrol

[ccp4bb] RE : [ccp4bb] consistently missing eletron density

Dear Huiming, as Pavel said, to get a reasonable map you need to collect either higher-resolution data (that you do not have because of your crystal) or low-resolution data. Working with only intermediate-resolution data may give you ugly maps even when your phases are perfect. As an example,

Re: [ccp4bb] HOLE CHANNEL

Dear Dave, I afraid that this program is not maintained for many-many years “An algorithm to find channels and cavities within protein crystals (CHANNEL)”: Oleg S. Kisljuk, Galina S. Kachalova and Nadejda Ph. Lanina ; J. Mol. Graphics, 1994, vol12 knowing that the principal programming power

Re: [ccp4bb] atomic scattering factors in REFMAC

Dear all, Just as a historic reminder, I feel necessary to mention a key article on refinement, written by R.Aragwal (1978) in Acta Cryst A, where he used 1- and 2-gaussian atomic factors (obviously, less precise that 4 gaussians + constant but allowed him at that moment to accelerate as much

Re: [ccp4bb] proper or improper ncs?

Hi, everybody, In addition to all comments, just as a pleasure to remind an old-fashion no computer way to calculate the rotation angle. The trace of a rotation matrix (the sum of its diagonal elements) is always equal to 2*cos(kappa)+1. Calculate it yourself for kappa = 180° and compare with

[ccp4bb] RE : [ccp4bb] Envelope Phasing.

Dear David, I would remind that the molecular-replacement positionning of molecular envelopes and some methodological features (in comparison with a conventional MR) of this have been discussed in : Urzhumtsev Podjarny (1995). On the Solution of the Molecular Replacement Problem at Very Low

Re: [ccp4bb] hi - history of protein crystallization (should be : conversion of euler angles)

Dear Vijay Sorry for further troubles with the program. Could you send me (in a PRIVATE mail, out of CCP4bb) the tcl file that you prepared using my template ? With best wishes, Sacha Urzhumtsev De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de vijay srivastava Envoyé :

Re: [ccp4bb] Treating Missing Reflections as Zero or Fcalc

Dear Gregg and Tim, Thank you for an interesting discussion and data. It may be useful to point out, in particular for other readers of the CCP4bb, that there are a couple of relevant issues (the role of a few missed reflections on a quality of images and the choice of the cut-off level when

[ccp4bb] are mathematician scientists ?! (previously Free Reflections as Percent and not a Number)

Dear Tim, as you know I avoid making public comments and prefer enjoying the comments done by others, however this time is hard to resist :-) I was surprised by your mail : do you mean that mathematicians are NOT SCIENTISTS ?! Do you mean that they are nasty persons who fight against normal

Re: [ccp4bb] are mathematician scientists ?!

Dear Tim, sure - no any problem . It was a nice occasion to talk about our complementarity (and make a publicity of some excellent old papers) ! With best regards, be well ! Sacha PS : I am even less English native speaker De : CCP4 bulletin board

Re: [ccp4bb] Fwd: question about calculating electrostatic potentials

Dear Constance, your question means that you want to know the so-called quantile rank corresponding to the cut-off levels you have chosen (see the article in Acta Cryst D, D70, 2593-2606 (2014) that is talking specially about this). To rescale from sigma's into percentile ranks, you may use

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

not know... However, I agree, you question is fully valid and is interesting. All the best , Sacha De : hofkristall...@gmail.commailto:hofkristall...@gmail.com [hofkristall...@gmail.com] Envoyé : mercredi 4 février 2015 14:09 À : Alexandre OURJOUMTSEV; CCP4BB

Re: [ccp4bb] proton scattering by X-rays

Dear Jacob, there was a nice small computation project by Anne Bochow published in the CCP4 Newsletters (2005), http://www.ccp4.ac.uk/newsletters/newsletter42/content.html, communication 9, illustrating how strong and how confusing the ripples may be indeed; if you want I may send it

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

Dear Bernhard, For the unplaced model, it can only be a Babinet model to improve the scaling, This is not fully true, and the flat mask correction can be used as well. Please look : Fokine, A. Urzhumtsev, A.G. (2002) On the use of low resolution data for translation search in molecular

Re: [ccp4bb] crystal anisotropy measurement?

Dear Cosmo, you may calculate effective resolution of your data set along different directions using the program EFRESOL (article in press in J.Appl.Cryst., the method is described by Urzhumtseva et al., 2013, Acta Cryst D69, 1921-1934). You can download the program from

Re: [ccp4bb] phase shift vs non-isomorphism

Dear Phil, Gerard Bricogne pointed out a long time ago that the clearest comparison between two sets of phases is the complex correlation coefficient between two best structure factors ( m F exp(i phi) ) - this is equivalent to map correlation, but can be analysed in resolution bins. I'm not

Re: [ccp4bb] MOLREP self-rotation matrix

Re: [ccp4bb] MOLREP self-rotation matrix

Sorry for a bug with the previous (empty) mail . Here is the message : Dear Chen, there is a very old program CONVROT (Urzhumtseva Urzhumtsev, 1997, J.Appl.Cryst) that you can dowload from http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html (or if you want I can send you a copy

Re: [ccp4bb] phenix installtion problem

Dear Weifei, I am neither in the Phenix nor in the CCP4 teams so I let me remark that it does not look reasonable, just a few minutes after Tom Terwilliger's mail : I'll answer you on the Phenix BB as you've asked specific questions about Phenix tools. sending your mail (see below) asking

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

Dear Pascal, A while ago when I did my tests on MR at a very low resolution, I did it both with “shaped” envelopes and with the “flat” ones. It did work for both (with simulated data, which is obviously not the same as the experimental), but MR with the “shaped” models was more robust. Some

Re: [ccp4bb] wavelet application in CCP4

Dear Charles, if you are interested in applications of wavelets to macromolecular crystallography, you may look also at a slightly earlier publication by Vladimir Lunin Acta Cryst. (2000). A56, 73-84

Re: [ccp4bb] wavelet application in CCP4

Dear Charles, if you are interested in applications of wavelets to macromolecular crystallography, you may look also at a slightly earlier publication by Vladimir Lunin Acta Cryst. (2000). A56, 73-84

Re: [ccp4bb] wavelet application in CCP4

Dear Charles, if you are interested in applications of wavelets to macromolecular crystallography problems, you may look also at a slightly earlier publication by Vladimir Lunin in Acta Cryst (2000) A56, 73-84 "Fixed-scale wavelet-type approximation of periodic density distributions."

[ccp4bb] sorry for spamming

Dear all, sorry for spamming your mail boxes - there is a bug in our system. Best regards, Sacha

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Khoa Pham, the question of a formal definition of en "effective" resolution and its variability with space direction is discussed in a) Urzhumtseva, L., Klaholz, B.P., Urzhumtsev, A. (2013) " On effective and optical resolution of diffraction data sets". Acta Cryst., D69 , 1921-1934.

Re: [ccp4bb] looking for a link between diffraction resolution and order within the crystal

Dear Vincent, first, certainly, you can continue to a higher resolutions distinguishing further details : 3.3 A - nucleic acid pairs 1.2 A - atomic details 0.9 A - deformation density (by the way, there was a relevant work, I think, by E.Blanc and G.Bricogne beginning of 2000, about

Re: [ccp4bb] Table 1 successor in 3D?

Dear Bernhard and Gerard, congratulations for nice results that both you (and Gerard team) have been contributed and published ! Just a nice occasion to remind (and slightly correct Bernhard's message in that article) that the 'efficient resolution' that we suggested (2013) is NOT a single

Re: [ccp4bb] efresol download?

Dear Johan one more copy :-) Yes, you can get it from http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique2=en Sorry for inconvenience... Luca, Daniel and Pavel, m - Le 26 Oct 17, à 17:39, Hattne, Johan a écrit : > Dear all; > Would anybody know where

Re: [ccp4bb] efresol download?

Dear Johan one more copy :-) Yes, you can get it from http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique2=en Sorry for inconvenience and answering so late... Luca, Daniel and Pavel, many thanks for your help ! Sacha Urzhumtsev - Le 26 Oct 17, à 18:50, Hattne, Johan

Re: [ccp4bb] resolution

Dear Graeme, Right, but you are talking about weights that reflect the data quality and say nothing about that of the starting model ; however refinement is a comparison of a model with data. The higher resolution of the data, the more sensitive they to model imperfections. Refinement

Re: [ccp4bb] Figure of merit in refinement

Thank you, Eleanor, for an important reminder : obviously, one more recent and relevant paper is that by Read and McCoy (Acta Cryst, D, 2016) [ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784668/ | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784668/ ] With best wishes, Sacha -

Re: [ccp4bb] Figure of merit in refinement

Dear Andre, I would strongly advice you to look at the article by Lunin and Skovoroda (Acta Cryst, A, 1995) that addresses exactly your question: [ https://scripts.iucr.org/cgi-bin/paper?vs0124 | https://scripts.iucr.org/cgi-bin/paper?vs0124 ] The authors remind a very important point that

Re: [ccp4bb] Overrefinement considerations and Refmac5.

Dear Eleanor, dear Michel (?), A while ago we statistically analysed the distribution of R, Rfree and of their difference as a function of the logarithm of resolution (Urzhumtsev et al., 2009, Acta Cryst, D65, 1283-1291). In this log-scale, the mode values for all three are nearly linear

Re: [ccp4bb] Overrefinement considerations and Refmac5.

Thank you, Bernhard, for poining out this nice paper by Ian, one more that I missed previously. Best regards, Sacha Urzhumtsev - Le 6 Mar 20, à 19:15, Bernhard Rupp a écrit : > In addition to Sacha’s work there are a few older papers by Ian Tickle & Cie. > (summarized in BMC) and a

Re: [ccp4bb] How to compare between electron density maps?

Dear Murpholino, there is a couple of articles addressing specifically this issue : Urzhumtsev, A., Afonine, P.V., Lunin, V.Y., Terwilliger, T.C., Adams, P.D. (2014) " Metrics for comparison of crystallographic maps ". Acta Cryst., D70 , 2593-2606 Urzhumtseva, L., Urzhumtsev, A. (2016)

Re: [ccp4bb] real real-space-refinement

Dear Thierry, - Le 31 Juil 20, à 21:58, Fischmann, Thierry <22f7fda0a875-dmarc-requ...@jiscmail.ac.uk> a écrit : > Jim wrote: > “ technically, not in Phenix either. The real-space refinement in Phenix > simply > picks peaks in the density and then pulls nearby atoms toward them. .

Re: [ccp4bb] B-factors very high

Dear Eleanor, You are absolutely right. However, in Polygon, you could compare the models selected by resolution, by size, etc. I use this occasion to wish you and others a happy New Year ! Sacha Urzhumtsev - Le 4 Jan 21, à 15:44, Eleanor Dodson

Re: [ccp4bb] criteria to set resolution limit

Dear Tom, there are a couple of papers (essentially the first one) with a relevant discussion. Urzhumtseva_2013_ActaCryst_D69_1921-1934 Urzhumtseva_2015_J.Applied Cryst_48_589-597 If you wish I may send you the files (off list). With best regards, Sacha Urzhumtsev - Le 13 Sep 21,

Re: [ccp4bb] Validation of structure prediction

Hi, James, hi, everybody, somehow relevant to your, James, comments : >>> MPscore=0.426∗ln(1+clashscore)+0.33∗ln(1+max(0,rota_out−1))+0.25∗ln(1+max(0,rama_iffy−2))+0.5 >>> >>> I.E. What if we could train an AI to predict Rfree by looking at the >>> coordinates? if somebody missed, there

Re: [ccp4bb] Future Diffraction Methods

Hi, everybody, hi, Nukri and Pavel ! I fully agree with Pavel that, if the speakers are not exceptional, if they are (as usually) concentrated on their specific and narrow problems, cross-discipline meetings make us lost quite fast, they are annoying and useless. Richard Feynmann had the same

Re: [ccp4bb] Updated pbd metrics and other small things

Dear Rafael, if 15 years ago are better than 20, do you mean the article Urzhumtsev, Afonine & Adams (2009) " On the use of logarithmic scales for analysis of diffraction data ". Acta Cryst., D65 , 1283-1291 ? There are some numbers and also some analytic inter / extrapolations. With

Re: [ccp4bb] quantifying electron density

Dear Sriram, dear Jon, The sum of values of a map (always calculated at some finite resolution) is not the same as a sum of density values. In such maps, a contribution of each atom is a function oscillating with the distance to the atomic center. Even when the height of these ripples is

Re: [ccp4bb] Input from the community for panel session: Crystallography is Dead! Long Live Crystallography!

Happy New Year to everybody ! Health and peace ! Hi, Nicholas, Actually, the title : “Crystallography is Dead. Long Live Crystallography!” made me laugh. As you can find in Wikipedia : [ https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king! |