Re: [ccp4bb] determining the point group and the space group

Dear Gihan I would say collecting X-FEL data to solve a novel structure is unusual, as the real power of these machines is in time resolved experiments. If you have not already, I would recommend recording a fairly complete low dose data set on a synchrotron beamline with one or two of the crys

Re: [ccp4bb] xds_par licence expired error

Dear Nishant XDS always has an expiry date - you download a new version from http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html to replace the old version. I do not know if XDSGUI also has an expiry date This should not be a surprise - when you run XDS you will see something like [g

Re: [ccp4bb] According correct space group assignment...

Rafal, Unit cell parameters: if you look at the images, and all the reflections are integrated, you should see little blue boxes & no missed reflections - if this is correct then the P1 unit cell is probably correct Regarding the space group: for this case you may find NCS confusing the symmet

Re: [ccp4bb] Acceptable range of CC1/2

Usual recommendations are to have CC-half > 0.3 or 0.5 (these are usually not so far separated) For the most part the refinement software is smart enough to down-weight “noise” in the outer shell so there is very little penalty in including weak measurements, and you should put up a fight with

Re: [ccp4bb] Python3 and MTZ

Dear Kay, While I am obviously biased, I have to say that using cctbx (even if it is "old" Python) has a lot to be said for it - there are a lot of tools in there which are useful once you have read the reflection data & want to do crystallography. Re: Python 3: within xia2, DIALS and other

Re: [ccp4bb] Python3 and MTZ

IUC). Right? Pls ignore my ignorance; I'm a beginner in this area ... best, Kay On Wed, 6 Jun 2018 20:22:10 +, graeme.win...@diamond.ac.uk<mailto:graeme.win...@diamond.ac.uk> mailto:graeme.win...@diamond.ac.uk>> wrote: Dear Kay, While I am obviously biased, I have to

Re: [ccp4bb] Python3 and MTZ

_min=-5, data_max=5, n_slots=100) for c, v in zip(h.slot_centers(), h.slots()): print(c, v) thought it may help the discussion. best wishes Graeme > On 7 Jun 2018, at 11:43, Marcin Wojdyr wrote: > > On 7 June 2018 at 05:29, graeme.win...@diamond.ac.uk > wrote: >> Dear

Re: [ccp4bb] [ccp4bb] Oxford University Press

Jacob, This is a known thing in other circles - see e.g. https://arxiv.org/abs/1011.6590 "Extending ArXiv.org to Achieve Open Peer Review and Publishing Axel Boldt (Submitted on 23 Nov 2010) Today's peer review process for scientific articles is unnecessarily opaque and offe

Re: [ccp4bb] Should we still keep copies of all raw data?

Sergei, all, I for one would always recommend saving data - not least as this is the basis for your science and you may need to revisit it later, perhaps before or after publication. Re: (a) I know we’re all working on improving the methods but they are still have scope for improvement (b) obvi

Re: [ccp4bb] data processing with split/bad crystals

Dear Andreas, all, With DIALS, correct treatment of overlapping reflections is current work in progress - yes, you can index and refine two or more independent lattices, but running dials integration on this will probably not work as well as we'd like at the moment. It should do something sens

Re: [ccp4bb] Structure solution - hexapeptide

Kristof, Just checking - have you tried SHELXT? Feeding in umerged HKL file I appreciate that this is direct methods but the tool is pretty powerful Also: you could find processing the data with different tools helps… Best wishes Graeme (who dabbles in “small" molecule stuff, too) > On 2 Aug

Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice

Matthew, One SBGrid example I used for a workshop was https://data.sbgrid.org/dataset/218/ This has the “wrong” beam centre as understood by (me/dials/xia2) which causes a certain amount of fun, nice example for use of the reciprocal lattice viewer and image viewer in DIALS to make sensible ch

Re: [ccp4bb] VERY old mtz file..

Dear Pavol, Reading text files without any software is a neat trick, if you can do it. (no file on a computer is “human readable” - but many are encoded in a form which allows a wide range of general tools to display it, not just specialist crystallography software) ;-) I have to say, I am mo

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

Dear Raquel, For published structures you can publish the raw data, which means that somebody else is looking after it - for this I would say that the current front runner is Zenodo - https://zenodo.org/ - which is paid for by CERN / EU etc. so someone else is (currently) picking up the tab. T

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

Dear Tim, I do not think Zenodo is limited to Europeans - at least I could not find this on their policy page: http://about.zenodo.org/policies/ I know of plenty of uploads from Japan for example Best wishes Graeme On 29 Nov 2018, at 21:16, Tim Gruene mailto:tim.gru...@psi.ch>> wrote: Dear

Re: [ccp4bb] Apple deprecating OpenGL

Hi Rob, I would think that this phrase is the key one: "The move will mean that, while applications and games developed with OpenGL and OpenCL will continue to run, they will almost certainly become increasingly unreliable.” Given that (IIUC) most crystallographic software uses pretty basic op

Re: [ccp4bb] buying a cluster

HI James, Re: dissenting opinion I suspect that this conclusions depends very closely on (i) the shape of the problem and (ii) the extent to which the binary has been optimised for the given platform. I am pretty sure that there are some applications (heavily threaded, making extensive use o

Re: [ccp4bb] buying a cluster

Re: publishing benchmarks - great idea - expand on what James described earlier. Most programs are GHz dependent (for most “sensible” definitions of GHz (not the mega-hyper-pipeline stall prone P4 say) however I see your point that “threaded” and “optimised for vector systems (e.g. AVX512)” woul

Re: [ccp4bb] Live stream of CCP4 Study Weekend?

I have enabled Flash but just get a black rectangle and no sound… Guessing that using Chrome on OS X is not supported? :-( > On 9 Jan 2019, at 09:33, Marcin Wojdyr wrote: > > On Wed, 9 Jan 2019 at 10:28, Kay Diederichs > wrote: >> >> Sorry, I need some additional help with this. >> >> If I

Re: [ccp4bb] Open Access Repositories for Big Data?

Hi Aaron I would guess most places would start to want $$ for storing multiples of 100 GB Google, Amazon, Microsoft all offer this kind of thing. Getting the data in and out can be slow, and I would expect as the data size tends towards big and the time tends to a long time it would be comparab

Re: [ccp4bb] visualising anis B factors

Hi Eleanor, This is pretty routine in chemical crystallography using e.g. Olex2 or similar - they use thermal ellipsoids to represent the anisotropic B parameters. I am guessing though that for any non-trivially sized protein this would be quite a computational challenge? best wishes Graeme

Re: [ccp4bb] old data

Hi Dean Usually there is a serial number buried somewhere in the header - many are text headers though some have TIFF format binary headers. Often a timestamp as well though this is less common From there biosync may help e.g. http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european&s

Re: [ccp4bb] Thoughtful remark...

Dear Leo, I would argue that not getting diffraction would indicate that the sample under study is not a crystal ;-) That way the two scenarios are the same - in neither case do you have a crystal in the loop All the best Graeme > On 1 Feb 2019, at 08:42, CHAVAS Leonard > wrote: > > Dea

Re: [ccp4bb] Deposition requirement of anomalous pairs?

Hi Eleanor I’d raise you scaled but unmerged intensities :-) Best wishes Graeme On 20 Mar 2019, at 12:21, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: Wouldn't it be a good idea if the pdb required that data depo

Re: [ccp4bb] Backup of whole synchrotrons

While this may sound absurd, the principle of incremental backups can help out a great deal here. Like Apple’s Time Machine, all we need to do is store a copy of the things which have changed rather than the entire facility, which reduces the burden by at least a few orders of magnitude. Such ef

Re: [ccp4bb] installation of XDS

Hi Nadine The program is probably correct - I suspect you have no XDS.INP in there I recommend using e.g. generate_XDS.INP for this purpose https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP You may find the wider XDS wiki worth a read Best wishes Graeme On 2 Apr 20

[ccp4bb]

Hi Scott, You can run CAD two or more times - merge the columns incrementally (i.e. 1..9 then (1..9)+10..16) Best wishes Graeme On 10 May 2019, at 23:57, Scott Horowitz mailto:horow...@umich.edu>> wrote: Hi all, I’m trying to combine 16 datasets together using Cad, and it’s failing with the

Re: [ccp4bb] resolution

Hi Sam, If you have good data to 2A, then I cannot imagine throwing away a significant fraction of it (there are lot of spots from 2.5-2A) will make your model better Suggest reading http://scripts.iucr.org/cgi-bin/paper?S0907444913001121 All best Graeme On 5 Jul 2019, at 06:43, Sam Tang mai

Re: [ccp4bb] resolution

Pavel, Please correct if wrong, but I thought most refinement programs used the weights e.g. sig(I/F) with I/F so would not really have a hard cut off anyway? You’re just making the stats worse but the model should stay ~ the same (unless you have outliers in there) Clearly there will be a poi

Re: [ccp4bb] challenges in structural biology

Dear All, I have been enjoying “lurking” on this thread - some thoughts I love this approach to conference organising :-) You missed radiation damage from this list ;-) - is critically connected to isomorphism, resolution, serial methods and is probably the single greatest limitation on X-ra

Re: [ccp4bb] challenges in structural biology

Dear all While I am well aware as are many that complimentary methods offer a great deal these days, I think X ray diffraction is not a solved problem for the reasons originally enumerated by James amongst others I would also remind that the conference is Diffraction Methods in Structural Biol

Re: [ccp4bb] Better Beamline suggestion!

Chandra What you are looking for here is a beamline with a detector with many pixels (so you can resolve the long axis) and a multi-axis goniometer - probably a SmarGon / kappa and an Eiger 16M would make a good combination for this. Searching on http://biosync.sbkb.org/ Should allow you to m

Re: [ccp4bb] Semet derivative dying almost immediately in beam

Their web page indicates they’re running a 315, so there are limits on useful low dose data collection. If you can get to a beamline with a pixel array detector and mount your samples carefully you’ll probably get more from low dose methods. The key thing with this is minimising background from

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Hi Frank I think this is a feature of (c)truncate - to avoid actually absent reflections messing up the French & Wilson correction for present-but-weak-or-negative reflections they are chucked out. If you put data in e.g. P212121 into AIMLESS absent reflections will be written out. They only v