Re: [ccp4bb] Combating disinformation in science and other areas

The idea of "Global Sustainability" can be found in the documents for the noted projects, so the United Nations "Sustainable Development Goals" appear to be worth reviewing as background - even though it appears the UN or UNESCO (below) is irrelevant to them : “Transformation is the red thread

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

Adding to that literature list a bit outside : Merchant, A., Batzner, S., Schoenholz, S.S. et al. Quote: "... we show that graph networks trained at scale can reach unprecedented levels of generalization, improving the efficiency of materials discovery by an order of magnitude. " Scaling

Re: [ccp4bb] Structure prediction - waiting to happen

A quote comes to mind (I cannot resist) : "Now, my own suspicion is that the universe is not only queerer than we suppose, but queerer than we can suppose [...]" -J. B. S. Haldane "Possible Worlds" in Possible Worlds and Other Essays (1927), p. 286

Re: [ccp4bb] Structure prediction - waiting to happen

" Is there a canned consensus paragraph that one can add with references to grants " How about: “In general we look for a new law by the following process. First we guess it. Then we compute the consequences of the guess to see what would be implied if this law that we guessed is right. Then

Re: [ccp4bb] Off topic - 3D models demonstrating drug binding to students

These magnetically-linking atomically accurate single-atom models look interesting - but I understand they might be too detailed or might shift around inadvertently :Snatoms Online Store - Magnetic Molecular Models for Educationsnatoms.comI also cannot say I used them (but I am always looking for

Re: [ccp4bb] Another folding AI

And of course,"... all models are approximations. Essentially, all models are wrong, but some are useful. However, the approximate nature of the model must always be borne in mind"Box, G. E. P.; Draper, N. R. (1987)Empirical Model-Building and Response SurfacesJohn Wiley & Sons"Since all

Re: [ccp4bb] Another folding AI

[ emphasis/bold font is mine]: “In general we look for a new law by the following process. First we guess it. Then we compute the consequences of the guess to see what would be implied if this law that we guessed is right. Then we compare the result of the computation to nature, with

Re: [ccp4bb] New Ewald sphere teaching tool

Thank you very much for this delightful applet! -Bryan W. Lepore 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

Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

Greetings This enzyme meets none of the stipulations, but I will point out as it is somewhat unusual to find in a grocery store : A food product called Just Egg contains “transglutaminase” as an ingredient. Make of that what you will. -Bryan W. Lepore (No affiliation with Just Egg or anything

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

Greetings - one assumption of this proposal seems to be that only H. sapiens will spread and harbor (?) the one specifically designed virus. I apologize if this is naive, but what is the basis for a virus staying only in one species? Or, if the specifically designed virus only does nice good

Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

> On Dec 11, 2020, at 07:42, Phil Evans wrote: > > But I’ve always thought the more interesting question is “this is the > structure, what does it do?” It sounds compelling though, that methods of the sort implemented in the CASP work are perfectly poised to make progress on the question:

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

> On Dec 9, 2020, at 07:45, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > ... GDT_TS (Global Distance Test - Total Score - you can look it up on > Wikipedia Thanks, this is helpful. Wikipedia: “The primary GDT assessment uses only the alpha carbon

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

On Dec 9, 2020, at 07:16, Harry Powell wrote: > > ...the important thing is [...] they’ve done something that no-one else has > managed to do as well in spite of years of trying. What, precisely, is the “something”? Exactly how much better than second place? Was the scoring the same across

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

Greetings — I am interested to know more about the following points to understand the results : [1] How was the “C-alpha-IDDT” (Mariani et. al., Bioinformatics, 29(21), 2722-2728, 2013) used, as - if I understand, the unprecedented and exceptional prediction capabilities of AlphaFold2 - as

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Representation within tutors at workshops

Greetings - an important recent article from Science, I thought would be good to include as background reading: “NIH’s new cluster hiring program aims to help schools attract diverse faculty” “The National Institutes of Health (NIH) is hoping universities will use a controversial—and largely

[ccp4bb] Demonstrations of the Fourier series with epicycles

Greetings - I just learned about a nifty representation of the Fourier series using epicycles, perhaps the CCP4 readers would be interested in - there's an animated gif here : https://twitter.com/johncarlosbaez/status/1094671748501405696?lang=en This longer video shows more detail of this

Re: [ccp4bb] wavelength dependence of intensities - Summary

On Jan 28, 2017, at 06:32, Bryan Lepore <bryanlep...@gmail.com> wrote: > > can I get a little help? For instance, what is the reference? The reference is: Acta Cryst D71 1799 Free to download - thank you to all who helped. -Bryan

Re: [ccp4bb] wavelength dependence of intensities - Summary

> > On Jan 27, 2017, at 11:05, Tim Gruene wrote: > [...], and a > pointer to your article with its explanation > http://dx.doi.org/10.1107/S1399004715011803: > [...] Apologies, but the above link was not pointing to an article - and I tried so many times I think I'm being

Re: [ccp4bb] Absence of contact between layers in a crystal

[ example structures with disordered crystal contacts ] Yes and they all have a good bulk solvent correction. -Bryan

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

On Nov 28, 2014, at 00:22, Gregg Crichlow gregg.crich...@gmail.com wrote: ... The paper now has been published, ... PDB ID 4K9G. ... The primary citation in the PDB summary is (2014) INT J ONCOL. 45: 1457-1468 ... unless any others are worth mentioning here... -Bryan

Re: [ccp4bb] atomic coloring for the color blind

FYI Kevin Cowtan has a web page that discusses using color diagrams with respect to the color blind interpretation. http://www.ysbl.york.ac.uk/~cowtan/colour/colour.html -Bryan

Re: [ccp4bb] Crystallography Near Absolute Zero?

Coming next : Negative Absolute Temperature for Motional Degrees of Freedom http://m.sciencemag.org/content/339/6115/52

Re: [ccp4bb] Mac mini advice

On Jan 22, 2013, at 13:08, Nat Echols nathaniel.ech...@gmail.com wrote: On Tue, Jan 22, 2013 at 9:59 . I would definitely recommend maxing out the memory, but don't buy it from Apple - we were able to get 16GB from CDW for less than $100. I think it is just that Apple only offers the

Re: [ccp4bb] Mac mini advice

On Tue, Jan 22, 2013 at 1:40 PM, Phil Jeffrey pjeff...@princeton.eduwrote: I don't think that anybody has shown a significant performance difference on Apple memory vs a reasonable 3rd party supplier. Apple may potentially have better quality controls but places like Crucial essentially have

Re: [ccp4bb] relationship between resolution and B values

B-factor needs to be weighted by occupancy, I think. I think Moleman does it. -Bryan

Re: [ccp4bb] vitrification vs freezing

warning - tangential: Steven Pinker's talk/promo on his new-new book The Sense of Style : Scientific Communication for the 21st Century : * * http://video.mit.edu/watch/communicating-science-and-technology-in-the-21st-century-steven-pinker-12644/ -Bryan

Re: [ccp4bb] usefulness of cacodylate?

On Fri, Nov 9, 2012 at 7:26 AM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote Anybody know a) how hazardous is cacodylate? b) does it really matter for crystallization screens? [...] (We're being subjected to a safety review.) I know you are in the UK but this wouldn't have

Re: [ccp4bb] A case of post publication fraud...Re: [ccp4bb] Fwd: [ccp4bb] PNAS on fraud

On Fri, Oct 19, 2012 at 2:20 PM, Jrh jrhelliw...@gmail.com wrote: Dear Colleagues, A different type of, post publication, fraud is the case of the discovery of streptomycin. See :- http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61202-1/fulltext I can't resist posting

Re: [ccp4bb] Anaerobic glovebox crystal cryo-cooling

On Tue, Apr 24, 2012 at 10:20 AM, David Gallagher dt...@mrc-mbu.cam.ac.uk wrote: I've been using a Belle technologies anaerobic glovebox with in built microscope and liquid nitrogen dewar port [...]   plunging loops straight into vials preloaded into an ESRF puck why, why, why, and why?

Re: [ccp4bb] indexing(?) question in P21 - solved

On Thu, Apr 19, 2012 at 4:28 PM, wtempel wtem...@gmail.com wrote: I went ahead and explicitly applied that +0.5*a translation. [...] It turns out that after the origin shift, some distances between equivalent atoms of the two structures exceeded 3A I'd be interested to know if cphasematch

Re: [ccp4bb] very informative - Trends in Data Fabrication

On the topic of MX fraud : could not an encryption algorithm be applied to answer the question of truth or falsity of a pdb/wwpdb/pdbe entry? has anyone proposed such an idea before? for example (admittedly this is a mess): * a detector parameter - perhaps the serial number - is used as a public

Re: [ccp4bb] very informative - Trends in Data Fabrication

On Tue, Apr 3, 2012 at 5:16 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote: I'm not sure how encryption can solve a problem of truth or falsity. AFAIU any given checksum will tell you if a file is corrupted or not. My brain decided to interpret that as true or false. and  A person can

Re: [ccp4bb] very informative - Trends in Data Fabrication

On Sat, Mar 31, 2012 at 6:08 PM, Kevin Jin kevin...@gmail.com wrote: I have seen several stories like this. Here is an open letter to Nature. http://www.jinkai.org/AAD/AAD_letter_2_nature.html I'd like to understand this better : please explain precisely, on this forum, the connection being

Re: [ccp4bb] a small trick for protein and organic compound cocrystallization.

On Fri, Mar 30, 2012 at 4:02 AM, Kevin Jin kevin...@gmail.com wrote: Here is way I have used for [...] I hate to be a curmudgeon, but can a list member please explain why this is not specifically blogspam or spam - or whatever it is exactly? -Bryan

Re: [ccp4bb] a small trick for protein and organic compound cocrystallization.

On Fri, Mar 30, 2012 at 3:26 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: What's the harm? have you seen usenet/Google groups? -Bryan

Re: [ccp4bb] Archiving Images for PDB Depositions

not sure I follow this thread, but this table might be interesting : http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf from: Detection and correction of underassigned rotational symmetry prior to structure deposition B. K. Poon, R. W. Grosse-Kunstleve, P. H. Zwart and N. K.

Re: [ccp4bb] Cell Params as a Function of Temperature

On Tue, Oct 18, 2011 at 5:01 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: references studying variation in cell params systematically as a function of temperature, with many points on the curve (not just RT and 100K?) a well cited article, from 1992: Effects of temperature on

[ccp4bb] Could Biological Negative Results be published?

It would be important to recall the most famous null result : the Michelson-Morley experiment, published in The American Journal of Science, explained 18 years later.

[ccp4bb] ccp4i:buccaneer+refmac curiosity on Intel mac osx only

it seems that shift-double-clicking on a buccaneer+refmac job in ccp4i and rerunning it with everything the same (except output name) will produce results (c-alphas built, Rfree, etc.) that are non-identical after a few cycles. apparently this is holds for Intel mac osx 10.5 or 10.6 only, not

[ccp4bb] (i)mosflm indexing / cell refinement

I seem to have noticed that (i)mosflm can index on one image, or two images that are not related by 90 degrees. also, cell refinement sometimes splits up a set of frames into maybe 3 or four segments of e.g. a few degrees each. and of course, I can set it based on frames 90 degrees apart. reason

[ccp4bb] (i)mosflm preferences

can preferences go in .mosflm/.profile? or - is there a place to put global preferences e.g. something like y-scale_refine=0/ the .mos appears to be crystal-specific. -Bryan p.s: thanks DW AL HP JH for the interesting 'gain' comments.

[ccp4bb] mosflm gain

wondering if mosflm can automatically estimate the gain. i.e. i gather it is still estimated the usual way. -Bryan

[ccp4bb] mosflm image angles

can mosflm handle a dataset defined by images with correct but unequal oscillation angles in the image headers? -Bryan

[ccp4bb] scala : cornercorrect file

if anyone knows of a cornercorrect file I might be able to use in scala, perhaps for an adsc q[any], please let me know off-list if you don't mind. -Bryan

Re: [ccp4bb] xds question

On Tue, Feb 8, 2011 at 7:17 AM, Simon Kolstoe s.kols...@ucl.ac.uk wrote: XDS [...] signal/noise = -3.0. i'd be interested to know if there is an equivalent in scala... perhaps 'REJECT 6 ALL -8' -Bryan

Re: [ccp4bb] Merging data to increase multiplicity

On Jan 28, 2011, at 8:45, Bosch, Juergen jubo...@jhsph.edu wrote: Mark Robien and I did a systematic study on about 30 data sets while we were at SGPP. can you name the detector(s)? -Bryan

Re: [ccp4bb] Merging data to increase multiplicity

On Fri, Jan 28, 2011 at 9:35 AM, herman.schreu...@sanofi-aventis.com wrote: [...] due to the 3-dimensional profile fitting. what is the specific difference between 3-d profile fitting and using a sliding window of more than one image? -Bryan

Re: [ccp4bb] cmakereference : reading reflections

On Wed, Dec 15, 2010 at 6:10 AM, Kevin Cowtan cow...@ysbl.york.ac.uk wrote: Looks like you're missing  -colin-fo '/*/*/[F,SIGF]' that did it. i gather the input is much like buccaneer then. also - is 0.2 the latest version - and the only command line options in v0.2 (15/04/05) that i see

[ccp4bb] cmakereference : reading reflections

does cmakereference v0.2 in ccp4 6.1.13 require 'project', 'dataset' or 'crystal' to be in the .mtz? because i thought by default, these were eponymous e.g my .mtz - that has labels F and sigF - : * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 project

Re: [ccp4bb] Extracting information from set of pdbs.

On Thu, Dec 2, 2010 at 12:17 PM, Justyna Wojdyla jw...@york.ac.uk wrote: get values for chosen torsion angles of ligand ... moleman with a script. -Bryan

Re: [ccp4bb] Structure based and motif based sequence alignment

I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constant while extending the sequence only at the c-terminus. IIUC : profile 1 = *structure-based* sequence alignment i.e. from STAMP (THESEUS?) profile 2 = a huge

[ccp4bb] scala : error of Mean((I)/sd(I))

[ scala 3.3.16 ] in scala's final table, there's Mean((I)/sd(I)). i could be wrong, but the error of this measurement seems to me to exist, considering the uncertainty of sigma = 1 / sqrt( 2 (N-1) ) ... but its not clear where the logfile has the values of I or sigma and N that correspond to

[ccp4bb] mosflm : image-dependent mask?

[ mosflm 7.0.6 ] [ imosflm 1.0.4 ] wondering if users can define a mask to associate with specific frames. e.g. if theres something weird on one region of frame 23, make a mask to block that part out only, and for all other frames, use the default mask for beamstop shadow. AFAIK the only way to

Re: [ccp4bb] Strange spots

On Fri, Oct 29, 2010 at 4:25 PM, Ethan Merritt merr...@u.washington.edu wrote: You may laugh, but the Google finds hits on the topic here:   http://atlas-conferences.com/cgi-bin/abstract/cauu-47 anyone who made complete sense of that abstract is invited to go here :

[ccp4bb] tlsanl and phenix TLS results

[ ccp4 6.1.3 ] i have some phenix TLS tensors i'd like to evaluate in tlsanl [*]. are there specific conversions/transformations to be wary of when setting up the job or interpreting the output? -bryan [*] originally posted on phenix BB with some gory details.

Re: [ccp4bb] tlsanl *NOW ALSO REFMAC* and phenix TLS results

documentation then i conclude the TLS protocol in refmac is markedly different from phenix (i know this is not strictly a ccp4 question). cf. : refmac: TLS RANGE 'A 245.' 'A 252.' ALL ORIGIN14.019 -10.476 -35.068 T 0.4974 0.0372 0.3453 0.0674 0.2984 0.0431 L 21.5463

[ccp4bb] Fwd: [ccp4bb] tlsanl *NOW ALSO REFMAC* and phenix TLS results

On Thu, Oct 21, 2010 at 11:42 AM, Ian Tickle ianj...@gmail.com wrote: There are a number of things that don't look right here, both with the Refmac and the Phenix runs: [...] interesting, thanks for these comments.  S should not have been symmetrized to actually display the principal axes in

Re: [ccp4bb] quantum diffraction

btw, buckyballs have measurable wave properties. i think they are trying virus particles now.