Re: [ccp4bb] am I doing this right?
Dear All, In the context of this discussion, I suggest the readers / discussion participants to have a look at new ideas on: Information Content of images, SNR, DQEs, A priori Probabilities, Shannon's Channel Information capacity,etc., expressed in: Van Heel & Schatz, arXiv 2020. (There is also an easy-to-find Youtube lecture on the issue by "marin van heel"). Cheers, Marin On Tue, Oct 26, 2021 at 3:58 AM Jacob Keller wrote: > Hi All, > > haven't been following CCP4BB for a while, then I come back to this juicy > Holtonian thread! > > Sorry for being more practical, but could you use a windowed approach: > integrate values of the same pixel/relp combo (roxel?) over time (however > that works with frame slicing) to estimate the error over many frames, then > shrink the window incrementally, see whether the successive > plotted shrinking-window values show a trend? Most likely flat for > background? This could be used for the spots as well as background. Would > this lose the precious temporal info? > > Jacob > > On Fri, Oct 22, 2021 at 3:25 AM Gergely Katona > wrote: > >> Hi, >> >> >> >> I have more estimates to the same problem using a multinomial data >> distribution. I should have realized that for prediction, I do not have to >> deal with infinite likelihood of 0 trials when observing only 0s on an >> image. Whenever 0 photons generated by the latent process, the image is >> automatically empty. With this simplification, I still have to hide behind >> mathematical convenience and use Gamma prior for the latent Poisson >> process, but observing 0 counts just increments the beta parameter by 1 >> compared to the prior belief. With equal photon capture probabilities, the >> mean counts are about 0.01 and the std is about 0.1 with >> rate≈Gamma(alpha=1, beta=0.1) prior . With a symmetric Dirichlet prior to >> the capture probabilities, the means appear unchanged, but the predicted >> stds starts high at very low concentration parameter and level off at high >> concentration parameter. This becomes more apparent at high photon counts >> (high alpha of Gamma distribution). The answer is different if we look at >> the std across the detector plane or across time of a single pixel. >> >> Details of the calculation below: >> >> >> >> >> https://colab.research.google.com/drive/1NK43_3r1rH5lBTDS2rzIFDFNWqFfekrZ?usp=sharing >> >> >> >> 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 *On Behalf Of *Nave, >> Colin (DLSLtd,RAL,LSCI) >> *Sent:* 21 October, 2021 19:21 >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* Re: [ccp4bb] am I doing this right? >> >> >> >> Congratulations to James for starting this interesting discussion. >> >> >> >> For those who are like me, nowhere near a black belt in statistics, the >> thread has included a number of distributions. I have had to look up where >> these apply and investigate their properties. >> >> As an example, >> >> “The Poisson distribution is used to model the # of events in the >> future, Exponential distribution is used to predict the wait time until the >> very first event, and Gamma distribution is used to predict the wait time >> until the k-th event.” >> >> A useful calculator for distributions can be found at >> >> https://keisan.casio.com/menu/system/0540 >> >> a specific example is at >> >> https://keisan.casio.com/exec/system/1180573179 >> >> where cumulative probabilities for a Poisson distribution can be found >> given values for x and lambda. >> >> >> >> The most appropriate prior is another issue which has come up e.g. is a >> flat prior appropriate? I can see that a different prior would be >> appropriate for different areas of the detector (e.g. 1 pixel instead of >> 100 pixels) but the most appropriate prior seems a bit arbitrary to me. One >> of James’ examples was 10^5 background photons distributed among 10^6 >> pixels – what is the most appropriate prior for this case? I presume it is >> OK to update the prior after each observation but I understand that it can >> create di
[ccp4bb] Information, Resolution, FSC, ... All you ever wanted to know!
Dear All, We have just posted an important paper on Information Theory in the context of Harvesting new Information in the imaging sciences, in (arXiv)! Any image one collects in a microscope, or 3D image in X-ray tomography, X-ray crystallography, for example, is covered by this comprehensive theory. A list of issues discussed or new concepts introduced: Instrumental Resolution, Information Theory, Information Harvesting, Signal-to-Noise Ratio, SNR, Shannon Nyquist sampling theorem, Janus Apodization Rule, Abbe’s resolution, Number of degrees of Freedom, Gabor transforms, Local Information Density, LID, Results Resolution, Fourier Ring Correlation, Fourier Shell Correlation, DQE, Fourier Ring Information, The Isotropic Nyquist Frequency, Fourier Shell Information, Transducer Information Efficiency, TIE, Relative TIE, The Gabor-Heisenberg Uncertainty principle, Under-sampling, Wrap-around Artefacts, Viral Glycosylation, the Rose equation, R-factors Channel Capacity, CC50, etc … A 43-pages single-spacing long story, but it is accessible to most scientists working in this field and it does resolve many outstanding issues in the imaging sciences! Just reading the abstract is enough to get a gist of the port of the matter. More than just two pennies worth (we hope), Cheers Marin (PS: we have applied for the necessary patents...) https://arxiv.org/abs/2009.03223 Google "arXiv" for "Information: to Harvest, to Have and to Hold" by: Marin van Heel, and Michael Schatz or see my Twitter account! To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] [ccpem] Averaging data for gain correction
One more remark on the camera correction issue... The camera correction does actually matter quite a bit, especially where it concerns the movie alignments in the early phases of processing, as Tanaka mentioned too. What I want to point out here is that the effect of the camera correction needs to be judged directly at the camera level by the FRC, or better still, by the FRI (https://arxiv.org/abs/2009.03223) and not at the end of a long processing chain where the influence of tons of unrelated intermediate processing decisions have been made. (Yes the quality of the shoes of a football player has an influence on who wins the game, but blaming the outcome of a game on the quality of shoes of the football player..., well... ). Since the camera correction significantly influences the movie alignment procedures, and assuming all processing is done adhering to the appropriate sampling and processing rules, the main influence on the 3D output of the game will be in the number of particles effectively available for 3D reconstruction. That number will affect the FSC (Harauz & van Heel 1986), yes, but less than it will affect the R-weighted Fourier Shell Information FSI (https://arxiv.org/abs/2009.03223)! Bottom line: take care of your metrics and stick to the rules and you will win the game! Two more pennies on the issue, Marin On Mon, Sep 14, 2020 at 3:50 PM Thomas Cleveland wrote: > Thanks everyone for the tool suggestions and comments. I particularly > enjoyed the correction of Mars rover photos as an example. > > Summary: > >1. sum_all_tiffs in cisTEM >2. relion_estimate_gain >3. camera-correction command in IMAGIC ( >https://www.nature.com/articles/srep10317) > > Tom > > On Mon, Sep 14, 2020 at 2:11 PM Thomas Cleveland < > thomas.clevel...@gmail.com> wrote: > >> Hi all, >> >> I've heard of folks averaging an entire set of unaligned movie files in >> order to make a new gain reference after data collection. Can anyone >> comment on how well this works? Is there any command that does it in a >> really simple way? (I realize it would not be too hard to just loop through >> and average all the movies, but thought I would ask, in case this is >> already implemented in a tool somewhere). >> >> Best, >> Tom >> > > -- > > To unsubscribe from the CCPEM list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] [ccpem] Refinements against DeepEMhancer maps
Dear Wout, A suggestion from the inventor of the FRC/FSC: please read the discussions on using non-linear refinement procedures to optimise linear metrics beyond their defined validity range in: "Information: to Harvest, to Have and to Hold", by Marin van Heel & Michael Schatz. (https://arxiv.org/abs/2009.03223) Groet, Marin On Thu, Sep 10, 2020 at 4:26 PM Oosterheert, W. (Wout) wrote: > Dear all, > > > > Thank you very much for the insightful comments. Intuitively I would also > say that using a postprocessed map that is optimized to look more like a > protein model, shouldn’t be used to real-space refine the model. Therefore, > I’ll keep performing my real-space refinements in the experimental maps. > That being said, I would still very much recommend DeepEMhancer for model > building and for map visualization in ChimeraX; in my experience, the maps > look clean and less anisotropic. > > > > Best, > > Wout > > > > *Wout Oosterheert; PhD Candidate; Crystal and Structural Chemistry; > Bijvoet Center for Biomolecular Research; Utrecht University; The > Netherlands* > > > > *From:* Collaborative Computational Project in Electron cryo-Microscopy < > cc...@jiscmail.ac.uk> *On Behalf Of *Schmid, Michael F. > *Sent:* Thursday, 10 September 2020 20:09 > *To:* cc...@jiscmail.ac.uk > *Subject:* Re: [ccpem] Refinements against DeepEMhancer maps > > > > Hi- > > I like to remind that what we are doing in EM is not refinement, in the > crystallographic sense, but model optimization into whatever map we are > using. > > And as for the dependence on resolution, a difference of 0.2 Å (I won’t > call it an error, since highly refined coordinates can vary this much, at a > 2 sigma, 5%, frequency) will not be detectable in the FSC at 2.5 Å, but > will start to give bad correlations at high resolution in a 1.2 Å map. The > model has to be more correct at high resolution to give a good FSC than it > has to be at low resolution, but this is obvious. > > Mike > > > > *From: *Collaborative Computational Project in Electron cryo-Microscopy < > cc...@jiscmail.ac.uk> on behalf of "Pintilie, Greg" < > 42742b50396d-dmarc-requ...@jiscmail.ac.uk> > *Reply-To: *"Pintilie, Greg" > *Date: *Thursday, September 10, 2020 at 10:52 AM > *To: *"cc...@jiscmail.ac.uk" > *Subject: *Re: [ccpem] Refinements against DeepEMhancer maps > > > > > > I fully second Marta's comment; why not use the full information to build > a more accurate model. Just watch out for over-sharpening, it's typically > easy to detect visually in the form of disconnected densities; unless you > have a 1.22Å map, then disconnected densities are OK :) > > > > Whether to use in refinement is a trickier question, because you can get > stuck in local minima easier when there is more detail. It could help to > start refining in the less detailed map, and then move to the more detailed > map. Use manual adjustments in Coot/ISOLDE to get out of local minima... > > > > Lastly, if we are using a real-space score, but get lower scores when > there is more detail in real-space, then I suppose we might have some > questions about whether that's a good score to use? > > > > Kindly, > > > > Greg > > > > > -- > > *From:* Collaborative Computational Project in Electron cryo-Microscopy < > cc...@jiscmail.ac.uk> on behalf of Marta Martinez > *Sent:* Thursday, September 10, 2020 12:59 PM > *To:* cc...@jiscmail.ac.uk > *Subject:* Re: [ccpem] Refinements against DeepEMhancer maps > > > > Hi all, > > I have also used DeepEMhancer, as well as other sharpening methods, > and I usually consider sharpened maps as a good help for tracing in > Coot. They contribute to solve quite a few ambiguities. Normally, I > have both the experimental map (coming from Relion in your case) as > well as the sharpened map (one or several) aligned together to > constantly assess the reliability of the improvements of tracing that > I can get with the sharpened maps, especially in controversial areas. > > Commonly, I perform the tracing in Coot based on the sharpened maps. > Regarding refinement, in automatic refinement steps, however, I only > consider the experimental map and all my validation scores are > referred to that map (higher CC is normal). Nevertheless, small > corrections of manual refinement are also performed in Coot and then > the sharpened maps are again a good help. As you might have > experienced, several rounds of automatic and manual refinement are > common to constantly improve the validation scores (referred to the > geometry o
Re: [ccp4bb] Which resolution?
> Dept. Microbiology & Cell Science, IFAS, UF > > > On 2/23/20, 2:42 PM, "Collaborative Computational Project in Electron > cryo-Microscopy on behalf of Gerard Bricogne" behalf of g...@globalphasing.com> wrote: > > [External Email] > > Gentlemen, > > Please consider for a moment that by such intemperate language and > tone, you are making a topic of fundamental importance to both the MX > and > the EM communities into a no-go area. This cannot be good for anyone's > reputation nor for the two fields in general. It has to be possible to > discuss the topic of "resolution" in a dispassionate way, so as to > jointly > gain an improved and shared understanding of the matter, without > feeling > implicitly under pressure to support one side or the other. An > acrimonious > dispute like this one can only be putting people off getting involved > in the > discussion, which is exactly the opposite of what a thread on a > scientific > bulletin board should be doing. > > > With best wishes, > > Gerard. > > -- > On Sun, Feb 23, 2020 at 08:15:34AM -0300, Marin van Heel wrote: > > Hi Carlos Oscar and Jose-Maria, > > > > I choose to answer you guys first, because it will take little of my > time > > to counter your criticism and because I have long since been less > than > > amused by your published, ill-conceived criticism: > > > > “*Marin, I always suffer with your reference to sloppy statistics. > If we > > take your paper of 2005 where the 1/2 bit criterion was proposed, > Eqs. 4 to > > 15 have completely ignored the fact that you are dealing with Fourier > > components, that are complex numbers, and consequently you have to > deal > > with random variables that have TWO components, which moreover the > real and > > imaginary part are not independent and, in their turn, they are not > > independent of the nearby Fourier coefficients so that for computing > radial > > averages you would need to account for the correlation among > coefficients*” > > > > I had seen this argumentation against our (2005) paper in your > > manuscript/paper years back. I was so stunned by the level of > > misunderstanding expressed in your manuscript that I chose not to > spend any > > time reacting to those statements. Now that you choose to so openly > display > > your thoughts on the matter, I have no other choice than to spell > out your > > errors in public. > > > > > > > > All complex arrays in our 2005 paper are Hermitian (since they are > the FTs > > of real data), and so are all their inner products. In all the > integrals > > over rings one always averages a complex Fourier-space voxel with its > > Hermitian conjugate yielding *ONE* real value (times two)! Without > that > > Hermitian property, FRCs and FSCs, which are real normalised > correlation > > functions would not even have been possible. I was - and still am - > stunned > > by this level of misunderstanding! > > > > > > > > This is a blatant blunder that you are propagating over years, a > blunder > > that does not do any good to your reputation, yet also a blunder > that has > > probably damaged to our research income. The fact that you can > divulgate > > such rubbish and leave it out there for years for referees to read > (who are > > possibly not as well educated in physics and mathematics) will do – > and may > > already have done – damage to our research. An apology is > appropriate but > > an apology is not enough. > > > > > > > > Maybe you should ask your granting agencies how to transfer 25% of > your > > grant income to our research, in compensation of damages created by > your > > blunder! > > > > > > > > Success with your request! > > > > > > > > Marin > > > > > > > > PS. You have also missed that our 2005 paper explicitly includes the > > influence of the size of the object within the sampling box (your: > “*they > > are not independent of the nearby Fourier coefficients*”). I remain > > flabbergasted. > > > > On Fri, Feb 21, 2020 at 3:15 PM Carlos Oscar Sorzano < > c...@cnb.csic.es> > > wrote: > > > > > D
Re: [ccp4bb] [3dem] Which resolution?
d its expectation value, so the overall > nonlinearity of the correlation isn't a concern. > > > > > -- > Steven Ludtke, Ph.D. Baylor > College of Medicine > Charles C. Bell Jr., Professor of Structural Biology > Dept. of Biochemistry and Molecular Biology ( > www.bcm.edu/biochem) > Academic Director, CryoEM Core( > cryoem.bcm.edu) > Co-Director CIBR Center( > www.bcm.edu/research/cibr) > > > > On Feb 21, 2020, at 10:34 AM, Alexis Rohou wrote: > > CAUTION:*** This email is not from a BCM Source. Only click links or > open attachments you know are safe.* > -- > Hi all, > > For those bewildered by Marin's insistence that everyone's been messing up > their stats since the bronze age, I'd like to offer what my understanding > of the situation. More details in this thread from a few years ago on the > exact same topic: > https://mail.ncmir.ucsd.edu/pipermail/3dem/2015-August/003939.html > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_pipermail_3dem_2015-2DAugust_003939.html=DwMFaQ=ZQs-KZ8oxEw0p81sqgiaRA=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc=UWn2RUCMENrXjn3JLSwlIU6Zmp_JYnRrXesjtsM1u2E=CZ3YcAV1LVKXsLT0KjCIRby6j3XPA6GqZcOVP3nMyK0=> > https://mail.ncmir.ucsd.edu/pipermail/3dem/2015-August/003944.html > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_pipermail_3dem_2015-2DAugust_003944.html=DwMFaQ=ZQs-KZ8oxEw0p81sqgiaRA=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc=UWn2RUCMENrXjn3JLSwlIU6Zmp_JYnRrXesjtsM1u2E=oG6lGnei74jC5VVGsfFAdiTpIxrZhs_IH2mH0re5QRM=> > > Notwithstanding notational problems (e.g. strict equations as opposed to > approximation symbols, or omission of symbols to denote estimation), I > believe Frank & Al-Ali and "descendent" papers (e.g. appendix of Rosenthal > & Henderson 2003) are fine. The cross terms that Marin is agitated about > indeed do in fact have an expectation value of 0.0 (in the ensemble; if the > experiment were performed an infinite number of times with different > realizations of noise). I don't believe Pawel or Jose Maria or any of the > other authors really believe that the cross-terms are orthogonal. > > When N (the number of independent Fouier voxels in a shell) is large > enough, mean(Signal x Noise) ~ 0.0 is only an approximation, but a pretty > good one, even for a single FSC experiment. This is why, in my book, > derivations that depend on Frank & Al-Ali are OK, under the strict > assumption that N is large. Numerically, this becomes apparent when Marin's > half-bit criterion is plotted - asymptotically it has the same behavior as > a constant threshold. > > So, is Marin wrong to worry about this? No, I don't think so. There are > indeed cases where the assumption of large N is broken. And under those > circumstances, any fixed threshold (0.143, 0.5, whatever) is dangerous. > This is illustrated in figures of van Heel & Schatz (2005). Small boxes, > high-symmetry, small objects in large boxes, and a number of other > conditions can make fixed thresholds dangerous. > > It would indeed be better to use a non-fixed threshold. So why am I not > using the 1/2-bit criterion in my own work? While numerically it behaves > well at most resolution ranges, I was not convinced by Marin's derivation > in 2005. Philosophically though, I think he's right - we should aim for FSC > thresholds that are more robust to the kinds of edge cases mentioned above. > It would be the right thing to do. > > Hope this helps, > Alexis > > > > On Sun, Feb 16, 2020 at 9:00 AM Penczek, Pawel A < > pawel.a.penc...@uth.tmc.edu> wrote: > >> Marin, >> >> The statistics in 2010 review is fine. You may disagree with assumptions, >> but I can assure you the “statistics” (as you call it) is fine. Careful >> reading of the paper would reveal to you this much. >> >> Regards, >> Pawel >> >> On Feb 16, 2020, at 10:38 AM, Marin van Heel < >> marin.vanh...@googlemail.com> wrote: >> >> >> >> * EXTERNAL EMAIL * >> Dear Pawel and All others >> >> This 2010 review is - unfortunately - largely based on the flawed >> statistics I mentioned before, namely on the a priori assumption that the >> inner product of a signal vector and a noise vector are ZERO (an >> orthogonality assumption). The (Frank & Al-Ali 1975) paper we have refuted >> on a number of occasions (for example in 2005, and most recently in our >> BioRxiv paper) but you stil
Re: [ccp4bb] [3dem] Which resolution?
Hi Pawel, We can indeed agree to disagree upon many basic things in life. We apparently disagree on the basic assumptions upon which you choose to build your science! What I am criticising is the very foundation you use to construct your science, namely the flawed Frank & Al-Ali (1975) formula relating SNR and CCC! Agreed, their errors are not of your making and not your responsibility! It is, however, your choice and your judgement to build upon that flawed foundation. At the end of the day, your construct, even when based on shaky foundations created by others, will remain your responsibility! Sorry, Marin On Sun, Feb 16, 2020 at 1:59 PM Penczek, Pawel A < pawel.a.penc...@uth.tmc.edu> wrote: > Marin, > > The statistics in 2010 review is fine. You may disagree with assumptions, > but I can assure you the “statistics” (as you call it) is fine. Careful > reading of the paper would reveal to you this much. > > Regards, > Pawel > > On Feb 16, 2020, at 10:38 AM, Marin van Heel > wrote: > > > > * EXTERNAL EMAIL * > Dear Pawel and All others > > This 2010 review is - unfortunately - largely based on the flawed > statistics I mentioned before, namely on the a priori assumption that the > inner product of a signal vector and a noise vector are ZERO (an > orthogonality assumption). The (Frank & Al-Ali 1975) paper we have refuted > on a number of occasions (for example in 2005, and most recently in our > BioRxiv paper) but you still take that as the correct relation between SNR > and FRC (and you never cite the criticism...). > Sorry > Marin > > On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A < > pawel.a.penc...@uth.tmc.edu> wrote: > >> Dear Teige, >> >> I am wondering whether you are familiar with >> >> Resolution measures in molecular electron microscopy. >> Penczek PA. Methods Enzymol. 2010. >> Citation >> >> Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8. >> >> You will find there answers to all questions you asked and much more. >> >> Regards, >> Pawel Penczek >> >> >> Regards, >> Pawel >> ___ >> 3dem mailing list >> 3...@ncmir.ucsd.edu >> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem=DwMFaQ=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI=3-TZcohYbZGHCQ7azF9_fgEJmssbBksaI7ESb0VIk1Y=XHMq9Q6Zwa69NL8kzFbmaLmZA9M33U01tBE6iAtQ140=> >> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
gi-bin/paper?S0907444903004219 > > > > Greetings, > > John > > > > Emeritus Professor John R Helliwell DSc > > > https://www.crcpress.com/The-Whats-of-a-Scientific-Life/Helliwell/p/book/9780367233020 > > > > > > > > > On 17 Feb 2020, at 11:26, "colin.n...@diamond.ac.uk" < > colin.n...@diamond.ac.uk wrote: > > > > > > Dear all. > > Would it help to separate out the issue of the FSC from the value of the > threshold? My understanding is that the FSC addresses the spatial > frequency at which there is a reliable information content in the image. > This concept should apply to a wide variety of types of image. The issue is > then what value of the threshold to use. For interpretation of protein > structures (whether by x-ray or electron microscopy), a half bit threshold > appears to be appropriate. However, for imaging the human brain (one of > Marin’s examples) a higher threshold might be adopted as a range of > contrasts might be present (axons for example have a similar density to the > surroundings). For crystallography, if one wants to see lighter atoms > (hydrogens in the presence of uranium or in proteins) a higher threshold > might also be appropriate. I am not sure about this to be honest as a 2 bit > threshold (for example) would mean that there is information to higher > resolution at a threshold of a half bit (unless one is at a diffraction or > instrument limited resolution). > > > > Most CCP4BBers will understand that a single number is not good enough. > However, many users of the protein structure databases will simply search > for the structure with the highest named resolution. It might be difficult > to send these users to re-education camps. > > > > Regards > > Colin > > > > *From:* CCP4 bulletin board *On Behalf Of *Petrus > Zwart > *Sent:* 16 February 2020 21:50 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] [3dem] Which resolution? > > > > Hi All, > > > > How is the 'correct' resolution estimation related to the estimated error > on some observed hydrogen bond length of interest, or an error on the > estimated occupancy of a ligand or conformation or anything else that has > structural significance? > > > > In crystallography, it isn't really (only in some very approximate > fashion), and I doubt that in EM there is something to that effect. If you > want to use the resolution to get a gut feeling on how your maps look and > how your data behaves, it doesn't really matter what standard you use, as > long as you are consistent in the use of the metric you use. If you want to > use this estimate to get to uncertainties of model parameters, you better > try something else. > > > > Regards > > Peter Zwart > > > > > > > > On Sun, Feb 16, 2020 at 8:38 AM Marin van Heel < > 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote: > > Dear Pawel and All others > > This 2010 review is - unfortunately - largely based on the flawed > statistics I mentioned before, namely on the a priori assumption that the > inner product of a signal vector and a noise vector are ZERO (an > orthogonality assumption). The (Frank & Al-Ali 1975) paper we have refuted > on a number of occasions (for example in 2005, and most recently in our > BioRxiv paper) but you still take that as the correct relation between SNR > and FRC (and you never cite the criticism...). > > Sorry > > Marin > > > > On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A < > pawel.a.penc...@uth.tmc.edu> wrote: > > Dear Teige, > > > > I am wondering whether you are familiar with > Resolution measures in molecular electron microscopy. > > Penczek PA. Methods Enzymol. 2010. > Citation > > Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8. > > > > You will find there answers to all questions you asked and much more. > > > > Regards, > > Pawel Penczek > > > > Regards, > > Pawel > > ___ > 3dem mailing list > 3...@ncmir.ucsd.edu > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > > -- > > > P.H. Zwart > Staff Scientist > > Molecular Biophysics and Integrated Bioimaging & > > Center for Advanced Mathematics for Energy Research Applications > > Lawrence Berkeley National Laboratories > 1
Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
Dear Colin
Great that you mention the Rose equation and its consequences for cryo-EM!
I have actually written a paper on that topic some 40 years ago [Marin van
Heel: Detection of object in quantum-noise limited images. Ultramicroscopy
8 (1982) 331-342]. I honestly have not thought about it for a long time
but I have recently been thinking about revisiting the topic. It remains
one of the very first particle-picking papers ever, and certainly still one
of the very best (and reference free) ones [Afanasyev 2017].
I remember I was very pleased when I realised one could calculate local
variances rapidly using fast convolutions! I remember the very moment in
December 1979, while visiting my parents in their house in Spain and
catching a bit of winter sunshine, leaning against the wall of their house
with my eyes half closed, that the “Aha-Erlebnis” struck. Thank you for
reminding me to go back to that issue!
Cheers
Marin
On Mon, Feb 17, 2020 at 2:36 PM colin.n...@diamond.ac.uk <
colin.n...@diamond.ac.uk> wrote:
>
>
> Dear Marin
>
> For electron microscopy, the Rose criterion (a measure of contrast/noise)
> is sometime used to distinguish low contrast features within polymers (see
> for example Libera, M. & Egerton, R. (2010). *Polymer Reviews*. *50*,
> 321-339.). A particular value of the Rose criterion implies a particular
> information content.
>
> I think this can be directly related to a particular threshold for FSC or
> FRC. If you can comment on this in your *Why-o-Why didactical crusade, I
> might even register for a twitter account!*
>
> *Regards*
>
> *Colin*
>
>
>
> *From:* CCP4 bulletin board *On Behalf Of *Marin
> van Heel
> *Sent:* 17 February 2020 13:29
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] [3dem] Which resolution?
>
>
>
>
>
>
>
> Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers)
>
>
>
> Resolution in the sense of the Abbe Diffraction Limit or the Rayleigh
> *Criterion
> are part of what we would now call the theory of linear systems, and are
> described by a “transfer function”. “Fourier Optics” covers the theory of
> linear systems in Optics. These two (essentially identical) resolution
> criteria state that the smallest details (let us call that “A(r)” for
> “Airy”) you can possible observe in real-space is inversely proportional to
> the size of the maximum aperture in Fourier space, i.e., the extent of the
> transfer function in Fourier space “T(f)”. This defines what “Instrumental
> Resolution” one could possibly achieve in an experiment, “instrumental” to
> differentiate it from the “Results Resolution” you actually managed achieve
> in your data collection/processing experiment [#Why-o-Why #10]. What a
> linear imaging system will do the image of the object (under the best of
> circumstances) is described by a (Fourier-space) multiplication of the
> Fourier transform of the object O(r) [= O(f)] with the (Fourier-space)
> transfer function T(f) of the instrument, yielding O’(f), which you need to
> transfer back to real space to obtain the exit wave in the image plane;
> that is: {O’(f)=T(f)·O(f)}. *
>
>
>
> *Note, however, that the properties of the sample, that is, of O(r), does
> nowhere appear in the transfer function T(f) or in its real-space version
> A(r)! The very concept of (instrumental) resolution is exactly that it
> does NOT depend on the object O(r)! The “results resolution” [#Why-o-Why
> #10], on the other hand, obviously depends on the sample; the illumination;
> on the radiation dose; the pH of the solvent; the air humidity; and the
> mood of the person doing the work on the day of preparation… *
>
>
>
> *The FRC/FSC “results resolution” measures we introduced in 1982/1986, fit
> perfectly in the abstract framework of linear systems and Fourier optics.
> The X-ray metrics like R-factor and phase-residuals and FOMs do NOT fit
> into that clean mathematical framework. Unfortunately, my EM colleagues
> started using X-ray metrics like “Differential Phase Residual” and “FOMs”
> in EM based on some gut feeling that the X-ray scientists know it better
> because they achieve a higher resolution than us EM blobologists. How wrong
> my EM colleagues were: the quality of the resolution metric is totally
> unrelated to the numerical resolution levels we operate at! Seeing 3mm
> kidney stones in a patient’s tomogram can be equally important as seeing *some
> hydrogen bond length in a cryo-EM density. The FRC/FSC actually make more
> sense than the indirect and hybrid X-ray ones. *This misconception has
> introduced a very tainted – and still ongoing – discussion in cryo-EM. Now
> that the fields of X-ray crystallography and cryo-EM are merging it is time
> to get things right! *
Re: [ccp4bb] [3dem] Which resolution?
Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers)
Resolution in the sense of the Abbe Diffraction Limit or the Rayleigh
*Criterion
are part of what we would now call the theory of linear systems, and are
described by a “transfer function”. “Fourier Optics” covers the theory of
linear systems in Optics. These two (essentially identical) resolution
criteria state that the smallest details (let us call that “A(r)” for
“Airy”) you can possible observe in real-space is inversely proportional to
the size of the maximum aperture in Fourier space, i.e., the extent of the
transfer function in Fourier space “T(f)”. This defines what “Instrumental
Resolution” one could possibly achieve in an experiment, “instrumental” to
differentiate it from the “Results Resolution” you actually managed achieve
in your data collection/processing experiment [#Why-o-Why #10]. What a
linear imaging system will do the image of the object (under the best of
circumstances) is described by a (Fourier-space) multiplication of the
Fourier transform of the object O(r) [= O(f)] with the (Fourier-space)
transfer function T(f) of the instrument, yielding O’(f), which you need to
transfer back to real space to obtain the exit wave in the image plane;
that is: {O’(f)=T(f)**·**O(f)}. *
*Note, however, that the properties of the sample, that is, of O(r), does
nowhere appear in the transfer function T(f) or in its real-space version
A(r)! The very concept of (instrumental) resolution is exactly that it
does NOT depend on the object O(r)! The “results resolution” [#Why-o-Why
#10], on the other hand, obviously depends on the sample; the illumination;
on the radiation dose; the pH of the solvent; the air humidity; and the
mood of the person doing the work on the day of preparation… *
*The FRC/FSC “results resolution” measures we introduced in 1982/1986, fit
perfectly in the abstract framework of linear systems and Fourier optics.
The X-ray metrics like R-factor and phase-residuals and FOMs do NOT fit
into that clean mathematical framework. Unfortunately, my EM colleagues
started using X-ray metrics like “Differential Phase Residual” and “FOMs”
in EM based on some gut feeling that the X-ray scientists know it better
because they achieve a higher resolution than us EM blobologists. How wrong
my EM colleagues were: the quality of the resolution metric is totally
unrelated to the numerical resolution levels we operate at! Seeing 3mm
kidney stones in a patient’s tomogram can be equally important as seeing *some
hydrogen bond length in a cryo-EM density. The FRC/FSC actually make more
sense than the indirect and hybrid X-ray ones. *This misconception has
introduced a very tainted – and still ongoing – discussion in cryo-EM. Now
that the fields of X-ray crystallography and cryo-EM are merging it is time
to get things right! *
*I guess I cannot yet terminate my #Why-o-Why didactical crusade: I will
need at least one more on just this linear-transfer theory issue alone…*
*Marin van Heel, CNPEM/LNNano, Campinas, Brazil *
On Sun, Feb 16, 2020 at 6:51 PM Petrus Zwart wrote:
> Hi All,
>
> How is the 'correct' resolution estimation related to the estimated error
> on some observed hydrogen bond length of interest, or an error on the
> estimated occupancy of a ligand or conformation or anything else that has
> structural significance?
>
> In crystallography, it isn't really (only in some very approximate
> fashion), and I doubt that in EM there is something to that effect. If you
> want to use the resolution to get a gut feeling on how your maps look and
> how your data behaves, it doesn't really matter what standard you use, as
> long as you are consistent in the use of the metric you use. If you want to
> use this estimate to get to uncertainties of model parameters, you better
> try something else.
>
> Regards
> Peter Zwart
>
>
>
> On Sun, Feb 16, 2020 at 8:38 AM Marin van Heel <
> 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Dear Pawel and All others
>>
>> This 2010 review is - unfortunately - largely based on the flawed
>> statistics I mentioned before, namely on the a priori assumption that the
>> inner product of a signal vector and a noise vector are ZERO (an
>> orthogonality assumption). The (Frank & Al-Ali 1975) paper we have refuted
>> on a number of occasions (for example in 2005, and most recently in our
>> BioRxiv paper) but you still take that as the correct relation between SNR
>> and FRC (and you never cite the criticism...).
>> Sorry
>> Marin
>>
>> On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A <
>> pawel.a.penc...@uth.tmc.edu> wrote:
>>
>>> Dear Teige,
>>>
>>> I am wondering whether you are familiar with
>>>
>>> Resolution measures in molecular electro
Re: [ccp4bb] [3dem] Which resolution?
Dear Pawel and All others This 2010 review is - unfortunately - largely based on the flawed statistics I mentioned before, namely on the a priori assumption that the inner product of a signal vector and a noise vector are ZERO (an orthogonality assumption). The (Frank & Al-Ali 1975) paper we have refuted on a number of occasions (for example in 2005, and most recently in our BioRxiv paper) but you still take that as the correct relation between SNR and FRC (and you never cite the criticism...). Sorry Marin On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A < pawel.a.penc...@uth.tmc.edu> wrote: > Dear Teige, > > I am wondering whether you are familiar with > > Resolution measures in molecular electron microscopy. > Penczek PA. Methods Enzymol. 2010. > Citation > > Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8. > > You will find there answers to all questions you asked and much more. > > Regards, > Pawel Penczek > > > Regards, > Pawel > ___ > 3dem mailing list > 3...@ncmir.ucsd.edu > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] [3dem] [ccpem] Which resolution?
Dear Pavel, Your paper is one of the more elaborate ones on the issue with an exhaustive list of references! No wonder, since some 20 years ago, Bruno Klaholtz was a very successful post-doc in my group at Imperial in London. However, I have discussed this paper with Bruno at our Brazil School in 2018 and I pointed out to him that your use of fixed-valued FSC thresholds makes that your paper, like 95% of the papers on resolution in our field, implicitly is based on the "sloppy statistics" of others, namely that the inner product between signal and noise vectors cannot be neglected. As long as those "sloppy statistics" papers are not taken from the literature, years or decades after they have been refuted, and the criticism against them is simply ignored or belittled, incorrect follow-up research along the same sloppy pathways is the consequence, and that is so sad... Sorry, Marin On Wed, Feb 12, 2020 at 8:34 PM Pavel Afonine wrote: > Interesting conversation! I see the 2017 paper is on bioRxiv. I wonder if > it ever made into a peer reviewed journal (couldn't find quickly)? > @Tim Gruene : have a look at d_model in > https://www.ncbi.nlm.nih.gov/pubmed/30198894 which is sort of along > similar lines of what you are hinting here. > Pavel > > On Wed, Feb 12, 2020 at 3:07 PM Marin van Heel < > 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Hi Tim, >> Good to hear from you! No longer at PSI?? >> See... You are already touching upon one of the logical breaking points >> in the resolutiton story...! X-ray crystallography resolution criteria >> like R-factors make absolutely no sense outside the field of >> crystallography and of structural biology. It is the result of a hybrid >> iterative optimisation process between the phases of a model structure and >> the measured amplitudes of a diffraction experiment! The FRC/FSC >> resolution criteria, in contrast, are universal quality metrics not at all >> coupled to Cryo-EM or structural biology. Using structural biology >> arguments like how well I see an alpha helix or how well I see the hole in >> an aromatic ring as an assessment criterion of whether a metric is good or >> not is a waste of time! (Moreover filtering a map can completley change >> its appearance without changing its information contents). Even some my own >> (ex-)students and (ex-)postdocs sometimes completely miss this fundamental >> point. The FRC and FSC criteria are now used as quality metrics in all >> walks of image science like X-ray tomography and super-resolution light >> microscopy, fields of science where atomic coordinates of proteins are not >> an issue. The FRC / FSC functions are universal and very direct metrics >> that compare both the amplitudes and the phases of two independent >> measurements of images or 3D-densities of the same object. For more >> details, see the 2017 bioRxiv paper and references therein ( >> https://www.biorxiv.org/content/10.1101/224402v1) and check my #WhyOWhy >> tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal >> structures: the final phases - Current opinion in structural biology 10 >> (2000) 259-264. >> >> Cheers, >> Marin >> >> >> On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene >> wrote: >> >>> Dear Marin, >>> >>> I did not read the enire thread, nor the manuscript you point at - >>> apologize >>> in case this has been discussed before. >>> >>> What about a practical approach to determine the resolution of a cryoEM >>> map: >>> one could take a feature with scales of interest, e.g. an alpha-helix, >>> and >>> shift and/or rotate it in steps of, say, 0.3A in several directions to >>> see, at >>> which magnitude (degree / distance) refinement does not take the helix >>> back to >>> its original position (within error margins). >>> >>> One could also take a Monte-Carlo approach and do an arbitrary number of >>> random re-orientations of such a helix, refine, and calculate the >>> variation in >>> position and rotation. >>> >>> This would reflect my understanding of resolution, much more than any >>> statistical descriptor. >>> >>> Best regards, >>> Tim >>> >>> On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote: >>> > Hi Laurence, >>> > >>> > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc >>> are >>> > also based on the same SLOPPY STATISTICS as are all fixed-valued FSC >>> > thresholds. This controversy h
Re: [ccp4bb] [3dem] [ccpem] Which resolution?
Hi Tim, Good to hear from you! No longer at PSI?? See... You are already touching upon one of the logical breaking points in the resolutiton story...! X-ray crystallography resolution criteria like R-factors make absolutely no sense outside the field of crystallography and of structural biology. It is the result of a hybrid iterative optimisation process between the phases of a model structure and the measured amplitudes of a diffraction experiment! The FRC/FSC resolution criteria, in contrast, are universal quality metrics not at all coupled to Cryo-EM or structural biology. Using structural biology arguments like how well I see an alpha helix or how well I see the hole in an aromatic ring as an assessment criterion of whether a metric is good or not is a waste of time! (Moreover filtering a map can completley change its appearance without changing its information contents). Even some my own (ex-)students and (ex-)postdocs sometimes completely miss this fundamental point. The FRC and FSC criteria are now used as quality metrics in all walks of image science like X-ray tomography and super-resolution light microscopy, fields of science where atomic coordinates of proteins are not an issue. The FRC / FSC functions are universal and very direct metrics that compare both the amplitudes and the phases of two independent measurements of images or 3D-densities of the same object. For more details, see the 2017 bioRxiv paper and references therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my #WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal structures: the final phases - Current opinion in structural biology 10 (2000) 259-264. Cheers, Marin On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene wrote: > Dear Marin, > > I did not read the enire thread, nor the manuscript you point at - > apologize > in case this has been discussed before. > > What about a practical approach to determine the resolution of a cryoEM > map: > one could take a feature with scales of interest, e.g. an alpha-helix, and > shift and/or rotate it in steps of, say, 0.3A in several directions to > see, at > which magnitude (degree / distance) refinement does not take the helix > back to > its original position (within error margins). > > One could also take a Monte-Carlo approach and do an arbitrary number of > random re-orientations of such a helix, refine, and calculate the > variation in > position and rotation. > > This would reflect my understanding of resolution, much more than any > statistical descriptor. > > Best regards, > Tim > > On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote: > > Hi Laurence, > > > > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc are > > also based on the same SLOPPY STATISTICS as are all fixed-valued FSC > > thresholds. This controversy has been ragings for a long long time and > the > > errors made were extensively described (again) in our most recent paper > > (Van Heel & Schatz 2017 BioRxiv: > > https://www.biorxiv.org/content/10.1101/224402v1) which has been > downloaded > > more than 3000 times. Further papers on the issue are in the pipeline. > The > > math BLUNDER behind this controversy is simple: the inner product > between > > a signal vector and a noise vector is NOT zero (but rather proportional > to > > SQRT(N) where N is the length of the vectors) and cannot be left out of > the > > equations. This error goes back to a paper published in Nature in 1975 > and > > has since been repeated frequently, including in the first paper > promoting > > the erroneous 0.143 FSC threshold. The consequences of this blunder in > > current processing are serious especially when these erroneous metrics > are > > used as an optimisation criterion in iterative refinements at resolutions > > close to Nyquist. I get tired of facing this systematic misuse of the > FSC > > function, which I myself have introduced into the literature in > 1982/1986, > > and people nevertheless feel they know better (with no scientific > arguments > > to support!) and they feel justified to use it beyond its definition > range, > > and to continue to ignore the correct math. To counter this systematic > > abuse of my brain child - over decades - I feel the need to use CLEAR > > LANGUAGE! > > Have fun! > > Marin > > -- > -- > 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/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Purchasing slides with diffraction gratings for teaching diffraction
Dear Pietro I have used many different gratings for the purpose over many years... Ones that I found very rewarding are writeable CDs and DVDs. They often come in a pack "protected" by a empty CD / DVD matrix hat is only plastic with grooves and no silver (or whatever the shiny recording material is). Burnig your own CDs DVDs has gone somwhat out of fashion so you may have a problem finding those transparent ones. But if you have a RED/GREEN laser pointer and empty CD / DVDs all kinds of diffraction experiments are possible. Since DVDs are designed for green/blue lasers, the red laser diffraction rapidly goes evanescent on a DVD. On the other hand a green or blue laser on a CD matrix gives you many diffraction orders on white wall in a dark lecture hall. Nylon flags and other woven materials can give excellent diffraction patterns. Great fun! Decades of students at Imperial and other places (www.brazil-school.org) enjoyed those crystallography/cryo-EM demos! My two cents, Marin On Tue, Mar 5, 2019 at 6:52 AM Roversi, Pietro (Dr.) wrote: > Dear all, > > I'd like to purchase slides with diffraction gratings for educational > purposes. > > Ideally, to be used with a visible-light laser pointer. > > And: with 1D and 2D patterns, of variable repeats - so as to be able to > illustrate the effect on the spacing in reciprocal space, as it were. > > I am looking online but not having much joy. > > Can anyone recommend a good provider to purchase from? > > Thank you! > > Pietro > > > Pietro Roversi > > LISCB Wellcome Trust ISSF Fellow > > https://bit.ly/2I4Wm5Z > > > Leicester Institute of Structural and Chemical Biology > Department of Molecular and Cell Biology, University of Leicester > Henry Wellcome Building > Lancaster Road, Leicester, LE1 7HB > England, United Kingdom > > Tel. +44 (0)116 2297237 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] 2019 New Year’s resolutions of a cryo-EM newbie
Hello Jacob I know it was a bit of a cynical joke and I know it does hurt ... After all my mother's Ellis Island records are dated 1923. Our last family reunion was 15 years ago in Illinois and Missouri. My Mid-West raised uncle was torpedoed off the coast of Cape Canaveral in 1942 transporting US military equipment. And, then again, my youngest son is a US citizen. At the same time, I also need to defend the integrity of scientific Canada in name of my late Canadian sister who was an excellent biochemist. And no, none of us were ever a member of the flat earth society (as far as I know)! ;) Lets hope for a happier 2019! Marin On Wed, Jan 2, 2019 at 11:07 AM Keller, Jacob wrote: > 6) I most sincerely hope that, if I stick to my five New Year’s > resolutions and stop wasting the cryo-EM community’s time, my fellow > Canadians will not extradite me to the fake-news country at our southern > border. > > > > > > I know this is a joke, but we in the USA are not a fake news people, and > please don’t punish us for the sins of our leadership--it’s painful for > many of us. > > > > JPK > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Position Available: HPC and Data-Processing Specialist (Campinas, Brazil)
POSITION AVAILABLE: HPC and Data-Processing Specialist (Campinas, Brazil) LNNano, CNPEM Campinas / São Paulo, Brazil. General job description - Support of HPC clusters and massive data storage, including: user support, installation and maintenance of programmes and libraries, participation in ongoing research and software development projects. - Provide training for internal/external users of our National Facility in using the HPC clusters and available programmes. Writing /maintaining user manuals. - Daily operation of the HPC clusters ( licences, repairs, contacts with hardware/software providers. - Supporting LNNano’s general IT activities and formulating policies (in conjunction with LNNano directors and the CNPEM general IT support group). - Providing support for meetings, courses, supporting WEB-site, and participating in dissemination activities of our HPC -elated scientific results. Qualification requirements - PhD in Computational Science, Computer engineering, Physics, Chemistry, Structural Biology, or related areas. - Experience in (parallel) programing in languages such as: C, C++; FORTRAN, CUDA, Python. - Post-doctoral research experience is an advantage - Experience in system-management of Linux OS environments. - English language proficiency Please send your CV and salary inquiries to: mariana.stevana...@cnpem.br <mailto:mariana.stevana...@cnpem.br>, subject line: “142376” == Cheers Marin -- == Prof Dr Ir Marin van Heel Laboratório Nacional de Nanotecnologia - LNNano CNPEM/LNNano, Campinas, Brazil tel: +55-19-3518-2316 Skype: Marin.van.Heel email: marin.vanheel(A_T)gmail.com <http://gmail.com> marin.vanheel(A_T)lnnano.cnpem.br <http://lnnano.cnpem.br> and: mvh.office(A_T)gmail.com <http://gmail.com> -- Emeritus Professor of Cryo-EM Data Processing Leiden University -- Emeritus Professor of Structural Biology Imperial College London Faculty of Natural Sciences email: m.vanheel(A_T)imperial.ac.uk <http://imperial.ac.uk> -- I receive many emails per day and, although I try, there is no guarantee that I will actually read each incoming email. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
