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

2019-11-25 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2019-11-28 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-02-28 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-02-05 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-02-06 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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??

2020-02-19 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-02-13 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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??

2020-02-19 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
(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

2020-01-14 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
!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

2020-01-14 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-03-28 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-03-30 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-05-11 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-03-19 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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?

2020-05-07 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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?

2020-05-07 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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] Question about small molecule crystallography

2020-06-08 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
, 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

2020-06-04 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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] number of frames to get a full dataset?

2020-06-30 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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?

2020-07-03 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-07-03 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-07-03 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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

2020-07-08 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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] CCP4 tutorials (files)

2020-07-30 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
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