Re: [ccp4bb] Xray-dataset usable despite low completeness ?

The data are > 90% complete at low resolution, where the completeness is more important, so this is probably fine - you would probably benefit from better detector placement in the future as the data are good to the edge. Was the detector offset or just too far away? 120° for an oP lattice

[ccp4bb] DIALS 2.0: from images to MTZ files with DIALS

Dear ccp4bb We are pleased to announce the release of - DIALS 2.0: a complete toolkit for processing of X-ray diffraction data from area detector images through to scaled intensities - free to all users and every line of code available for inspection at https://github.com/dials/dials. Thanks

Re: [ccp4bb] What resolution - X-ray diffraction round this time

Hi Dusan, I am pretty sure "It is well accepted that the criteria for resolution cutoff should consider both I/SigI and Rmerge for the outer most shell. For data sets collected at synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as a good practical reference.” has

[ccp4bb] Representation within tutors at workshops

Dear all, This is an interesting debate on a complex topic, which firstly I would like to slightly disentangle from the workshop itself - hence the subject change. I do this as some of the comments could be interpreted as directed specifically at the workshop organisers, which I do not feel is

Re: [ccp4bb] Representation within tutors at workshops

Dear Selina, All, Apropos: For one, there are expert users for the software taught at these courses. Often, the software developers know these persons, and it would be great if they could nominate at least one or two persons who could teach in their place, having gender balance and (age)

Re: [ccp4bb] MX data processing with GPUs??

Dear Ana, To follow up on the contributions from others, there are some particular annoyances with MX processing which differentiate it from other “big data” or imaging problems. In tomographic reconstruction you have a big block of data which needs to (as a simplistic approximation) be

Re: [ccp4bb] data processing

Dear Smita, You need only do a format conversion I expect, no processing required. For this you will want either f2mtz - http://www.ccp4.ac.uk/html/f2mtz.html or pointless - here use the -c option to copy rather than performing the analysis on the data

Re: [ccp4bb] MX data processing with GPUs??

(DLSLtd,RAL,LSCI) mailto:graeme.win...@diamond.ac.uk>> wrote: Dear Ana, To follow up on the contributions from others, there are some particular annoyances with MX processing which differentiate it from other “big data” or imaging problems. In tomographic reconstruction you have a big

Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

!s do not describe the data set that was actually used for structure solution and deposition! Eleanor On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) mailto:graeme.win...@diamond.ac.uk>> wrote: Dear Dave, Star Aniso Developers, If this turns out to be because we are “missing so

Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

Dear Dave, Star Aniso Developers, If this turns out to be because we are “missing something” i.e. there is an expectation on a property being present in the output files but it’s not there in our MTZ output, please let us know :-) Best wishes Graeme On 14 Jan 2020, at 09:06, David Lawson

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Hi John, Sure, happy to do this, just as soon as I figure how to do this automatically ;-) Thank you Gerard for your kind words - as people will note there are a couple of rough edges at the moment (as illustrated with typos) - however once these are tidied up I’ll circulate the location of

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

yone is interested please drop me a line off list All the best Graeme On 28 Mar 2020, at 06:12, Winter, Graeme (DLSLtd,RAL,LSCI) mailto:graeme.win...@diamond.ac.uk>> wrote: Hi John, Sure, happy to do this, just as soon as I figure how to do this automatically ;-) Thank you Gerard for

Re: [ccp4bb] DIALS error

Dear Maria Please could you send (off list) the 3_experiments,expt and 3_reflections.refl files? Happy to take a look. I expect it’s related to your experiment geometry (beam centre or similar) Thanks Graeme On 11 May 2020, at 14:22, Demou, Maria mailto:maria.demou...@ucl.ac.uk>> wrote:

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Hi Folks, Quick note on "Like a super raw image diet-plan for the incoming summer” - the bslz4 compression used with Eiger works really well, and the data are pretty close to entropy limit in terms of size - which means if you measure your data carefully (i.e. low background etc.) you can

Re: [ccp4bb] What refinement programs are fully Open Source?

Hi Pietro, To be precise, xia2 is a tool (which is open source under any definition - BSD licensed) for running data processing programs on your behalf. If you run with DIALS for indexing, integration and scaling (which are licensed the same way, and uses cctbx which is also open source) then

Re: [ccp4bb] What refinement programs are fully Open Source?

Dear Tim, While I agree that the papers describing XDS are excellent (and acknowledge precisely this every time I talk about DIALS!) I am certain that the actual implementation of XDS deviates significantly from the mathematical descriptions in the paper for the simple reason that writing data

Re: [ccp4bb] number of frames to get a full dataset?

Or, we could accept the fact that crystallographers are kinda used to multiplicity of an individual Miller index being different to multiplicity of observations, and in Table 1 know which one you mean?  Given that they add new information (at the very least to the scaling model) they are

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

Thanks Ian - I think you raise some excellent points - while I think the general reader (TM) would understand that redundancy and multiplicity mean broadly the same thing in Table 1, I think having program developers document _precisely_ what they mean by those values would be very valuable. I

Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

its! This may be related to sharing a window rather than the whole desktop > but something to be aware of. I have taken to using Zoom if I want to work > with others sharing an NX session. > > Cheers, > > James > > > -Original Message----- > From: CCP4 bulletin

Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

Hi Nick I’ll offer a vote in favour of teams, as it is possible with the desktop application to hand over control as well for a shared window (e.g. NX) so your student could perform the collection themselves under your supervision rather than just watching. I’ve not tried teams + NX as a

Re: [ccp4bb] Accessing full list of programs in CCP4I2

Hi Folks, Re: docs for elderly programs cd $CBIN/html In here you will find the ccp4 program docs probably going back ~ 20+ years for the old programs - for _your_ version of ccp4 It’s probably got greater coverage on the old command line stuff than the newfangled i2 things Cheers Graeme

Re: [ccp4bb] Question about small molecule crystallography

, bogba...@yahoo.co.uk<mailto:bogba...@yahoo.co.uk> wrote: Re: "it turns out to be very very easy to exceed the count rate where the detector electronics can keep up." Sorry if this is obvious, but I take it you mean "_can't_" keep up? Jon Cooper On 4 Jun 2020 13:0

Re: [ccp4bb] Question about small molecule crystallography

Dear All, A small word of caution regarding chemical crystallography on an MX-like beamline - if you have a bright source, a well diffracting crystal and a pixel array detector it is perfectly possible to lose counts in the strongest reflections without noticing - certainly without going over

Re: [ccp4bb] CCP4 tutorials (files)

Hi Rafael, http://legacy.ccp4.ac.uk/docs.php -> tutorials Looks like there’s something very broken with the style sheets or something but the information does appear to be available The links to tar files of data appear to work Best wishes Graeme On 30 Jul 2020, at 15:10, Rafael Marques

Re: [ccp4bb] Apple Silicon / XQuartz / X11 / CCP4

Hi Antony In theory (TM) things should just work with Rosetta 2 - how well they work is a matter for some debate and I think there will be a lot of eyes on non-Apple benchmarks of this system. I would guess though that it will be inevitable that we (DIALS, CCP4, the community, …) need to

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

Hi All, Sorry for the slow response - holiday season & all (I am sure many of us needed a break at the end of 2020) Windows is currently not super well supported for xia2 / DIALS work and won’t work at all for xia2 / XDS for the simple reason that XDS is not available for the platform (hence

Re: [ccp4bb] Should Rmerge be reported?

Tim, can I explain? To be honest no! Other than old habits and all. Should converge to the same value in the end, so you have a valid point. All the best Graeme From: Tim Gruene Sent: Thursday, June 10, 2021 14:02 To: Winter, Graeme (DLSLtd,RAL,LSCI) Cc

Re: [ccp4bb] Should Rmerge be reported?

Once again I find myself jumping to the defence of this rather poor statistic! Yes, Rmerge is a very poor estimator of "data quality" and has many well published flaws related to multiplicity, but the low resolution Rmerge, if combined with a multiplicity > (say) 5, is a good indicator of

Re: [ccp4bb] Should Rmerge be reported?

is an uphill battle. All the best Graeme From: Manfred S. Weiss Sent: 10 June 2021 13:43 To: Winter, Graeme (DLSLtd,RAL,LSCI) ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Should Rmerge be reported? Dear Graeme, a better number to look at is Isa. Instead of low

Re: [ccp4bb] How to process two datasets 45 degrees apart?

Process with the same starting orientation matrix in Mosflm, with XDS I would process one sweep then take the output of IDXREF and copy into the XDS.INP for second sweep using https://xds.mr.mpg.de/html_doc/xds_parameters.html#UNIT_CELL_A-AXIS= to ensure common axis definitions. Integrate

Re: [ccp4bb] Rmeas in DIALS?

Something odd happening there - please could you send the text log off list? i.e. xia2.txt Thanks Graeme On 1 Jul 2021, at 00:58, Murpholino Peligro mailto:murpholi...@gmail.com>> wrote: Why Rmeas is negative in DIALS output? Thanks To unsubscribe from

Re: [ccp4bb] Rmeas in DIALS?

-lmb.cam.ac.uk>> wrote: You can get a negative Rmeas in a shell where is negative Sent from my iPhone On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) mailto:graeme.win...@diamond.ac.uk>> wrote:  Thanks for sending the logs Looking at the output the negative R values don’t co

Re: [ccp4bb] Rmeas in DIALS?

I wonder, is ccp4i2 doing something itself which arrives at those numbers? i2 devs - thoughts? Thanks Graeme On 1 Jul 2021, at 05:49, Winter, Graeme (DLSLtd,RAL,LSCI) mailto:graeme.win...@diamond.ac.uk>> wrote: Something odd happening there - please could you send the text log off list

Re: [ccp4bb] am I doing this right?

This rang a bell to me last night, and I think you can derive this from first principles If you assume an observation of N counts, you can calculate the probability of such an observation for a given Poisson rate constant X. If you then integrate over all possible value of X to work out the

Re: [ccp4bb] Determining Second Lattice

If you are already using dials anyway, adding max_lattices=3 Say to the dials.index command line will probably do what you want You can also look at them all in the reciprocal lattice viewer. All the best Graeme > On 31 Aug 2023, at 09:20, Harry Powell >

Re: [ccp4bb] radiation damage and image discard

Along similar lines, if you happen to be working in the DIALS ecosystem there is the dials.damage_analysis program, which takes the scaled data (scaled.expt, scaled.refl) and computes a number of statistics including Rd as discussed below, and the cumulative-pairwise R factor Rcp, which

Re: [ccp4bb] Outlawed PDB files, what should a muggle do

Sent: 20 September 2023 16:35 To: Winter, Graeme (DLSLtd,RAL,LSCI) Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Outlawed PDB files, what should a muggle do gemmi convert --shorten 7qgf.cif foo.pdb ? -- David On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) <6a19cead4

[ccp4bb] Outlawed PDB files, what should a muggle do

Looks like PDB files have been outlawed because mmCIF But dimple needs PDB files cif2pdb says nope Grey-Area work :( $ cif2pdb --help * ERROR * No cif file read on input Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif * ERROR * No cif file read on input Grey-Area

Re: [ccp4bb] Database for submitting unprocessed diffraction data

Dear Mirek Scraping metadata from the image headers is a very nice idea I wonder, how sustainable is your system? For example would I be thanked or cursed for uploading substantial interesting data sets? One of the advantages of Zenodo, as much publicised and also highlighted by Loes, is the

[ccp4bb] DIALS 3.11 release: graphical utilities broken

Hello everyone including brave souls who are keen to use the latest greatest version of DIALS - the recently released 3.11 Sorry Please don’t We have had a couple of reports of issues with the graphical utilities in here caused by upstream changes in Python which have completely broken the

Re: [ccp4bb] Multiplicity is more than 20

Hi Prasun You just measured the reflections a lot. 33 is fine. More likely even with cubic space groups I’d love to know where you got the idea of the limit from. I have data sets with more than 100 fold multiplicity The R conversation I’ll leave to others Best wishes Graeme On 19 Sep 2022,

Re: [ccp4bb] Lower b-factors with increasing T

Hi Matt, You mention that you process with DIALS - one thing I would recommend is scaling all the data together then merging each temperature point separately - I could do with preparing a HOWTO on this [1] - this would then mean that they are being scaled to be as similar as possible before

Re: [ccp4bb] Lower b-factors with increasing T

Hi Harry, You’re not wrong - “conventional wisdom” these days is pointing to CC of about 0.3 but I suspect that the difference is pretty modest in general However, in the case, the difference could have an impact as the higher resolution reflections may have something to say about the overall

Re: [ccp4bb] Error while running BLEND

Hi Pedro Problem here is that ccp4.python is Python 3 and BLEND is still written for Python 2.7 This was one of the modernisation things which changed from 2 -> 3 An older version of ccp4 would probably still work - version 7.something Looks like BLEND needs to be updated… Best wishes

Re: [ccp4bb] DIALS 3.11 release: graphical utilities broken

, at 16:31, Winter, Graeme (DLSLtd,RAL,LSCI) <6a19cead4548-dmarc-requ...@jiscmail.ac.uk<mailto:6a19cead4548-dmarc-requ...@jiscmail.ac.uk>> wrote: Hello everyone including brave souls who are keen to use the latest greatest version of DIALS - the recently released 3.11 Sorry

Re: [ccp4bb] Future Diffraction Methods

Dear All, This was not really discussed widely at the study weekend however I think we have a core group of people who are sufficiently committed to the “GRC on diffraction methods” cause that we will keep it alive - as chair elect I also hold a very strong belief that we should keep this

[ccp4bb] Photographic museum of X-ray diffraction detectors

Season’s greetings everyone It is of course the season to be preparing CCP4 study weekend presentations…. and I was looking for some photographs of vintage beamline hardware and in particular detectors that I used in the dim and distant past. Does anyone have a photograph of SRS 7.2 with the

Re: [ccp4bb] Future Diffraction Methods

Hi All One of the joys of this meeting to me is that it is *not* about the science results and instead explicitly about how you get to those results. I worry that any meeting focussed on complimentary methods would inevitably coalesce around the common themes - science results - and become yet

[ccp4bb] Save the date! “Not the GRC” on Diffraction Methods in Structural Biology 2024

Good morning all, “Not the Gordon Research Conference” on Diffraction Methods in Structural Biology 2024 - Experiments and Measurements Organisers: Graeme Winter, Kunio Hirata (NTGRC-chairs) Helena Taberman, Ali Ebrahim (NTGRS-chairs) Local organisers - Arwen Pearson, Ashwin Chari As you

Re: [ccp4bb] Issues with viewing images with dials

HI Zoe If, from a terminal with CCP4 configured, you type dials.image_viewer (path-to-hdf5-master-file) Where (path-to-hdf5-master-file) is your file location, does it work? All the i2 message says is “something went wrong” which is not super helpful As a general rule, I also usually

Re: [ccp4bb] Is it possible to process master.h5 file using XDS Mac version (Intel)?

Dear Zhen It certainly is. You need a plug-in called neggia or durin to do this. You’ll find details on the XDS wiki which you can google for. Best wishes Graeme > On 3 Jun 2023, at 15:35, Zhen Gong wrote: > > I would like to process master.h5 file with XDS. This is the error message >

[ccp4bb] Patenting ligand binding?

Interesting https://www.freepatentsonline.com/20230228695.pdf Patent for use of electron diffraction to assess ligand binding Stumbled across this because the patent application cites my work - felt that this would be of interest to the community … discuss? Graeme -- This e-mail and any

Re: [ccp4bb] Patenting ligand binding?

can be patented? > > Cheers, > Tim > > > On Fri, 28 Jul 2023 07:45:38 + "Winter, Graeme (DLSLtd,RAL,LSCI)" > <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Interesting >> >> https://www.freepatentsonline.com/20230228695.p

[ccp4bb] Diffraction Methods 2024

Dear CCP4BB, As some of you may remember we are keeping the spirit of the GRC in diffraction methods in structural biology alive. Accordingly I would like to announce, on behalf of the meeting organisers Diffraction Methods 2024 Which will be held 22nd - 27th July 2024 at the Harnack House in

Re: [ccp4bb] Truncate / ctruncate / moments of E etc.

water...@gmail.com>> wrote: Norman Stein's article at the back of this newsletter is the one I like! https://legacy.ccp4.ac.uk/newsletters/newsletter47/newsletter47.pdf -- David On Wed, 14 Feb 2024 at 15:14, Winter, Graeme (DLSLtd,RAL,LSCI) <6a19cead4548-dmarc-requ...@jiscmai

Re: [ccp4bb] Truncate / ctruncate / moments of E etc.

. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> This has graphs: https://www.ccp4.ac.uk/html/pxmaths/bmg10.html . -- Ian On Wed, Feb 14, 2024 at 3:25 PM Winter, Graeme (DLSLtd,RAL,LSCI) <6a19cead4548-dmarc-requ...@jiscmail.ac.uk<mailto:6a19cead4548-dmar

[ccp4bb] Truncate / ctruncate / moments of E etc.

Good afternoon all, Chatting to someone and wanted to provide some pointers on how to interpret the moments of E from truncate or ctruncate, and realised that I don't have any good references​ for this to hand i.e. what I am looking for and why, and my google search didn't come up with much

[ccp4bb] i2 won't accept 90 degree angles in moniclinic

Tried reporting to i2 dev list but it got bounced - feels like something others may hit so don’t feel _too_ bad sending to the bb with a tiny attachment [cid:CA3CE9EB-841D-41A3-A41E-F79714492B21] Hi Folks Helping someone out with some rather specialist data processing challenges and she hit

Re: [ccp4bb] Diffraction Methods 2024

and Ashwin Chari From: diffmet2024-boun...@physnet.uni-hamburg.de on behalf of Winter, Graeme (DLSLtd,RAL,LSCI) Sent: 05 February 2024 09:56 To: CCP4BB@JISCMAIL.AC.UK Cc: diffmet2...@physnet.uni-hamburg.de Subject: [Diffmet2024] Diffraction Methods 2024 Dear CCP4BB

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

as here. Best wishes Graeme > On 23 Feb 2024, at 09:49, Huw Jenkins wrote: > > [You don't often get email from h.t.jenk...@me.com. Learn why this is > important at https://aka.ms/LearnAboutSenderIdentification ] > > Hi Graeme, > >> On 21 Feb 2024, at 16:52, Wint