Re: [ccp4bb] on mtz file

Dear Smith SIGFP should have come from the same source as FP – data reduction I would hope. You will need to find the original processed data to copy this column from. FOM should have come from the phasing process, but could equally be expressed in terms of HL coefficients A B C D

Re: [ccp4bb] Isomorphism

Equivalently you can push the whole lot into an aimless scaling run & look carefully at the logs - that’ll probably be more informative than pointless (or BLEND) for relatively large wedges of data PG622 will help you here it must be said! Best wishes Graeme > On 30 Sep 2015, at 11:10, Tim

Re: [ccp4bb] Advice for Structure Determination

Dear Monica Given you have eliminated all other phasing possibilities I would try phasing from native atoms e.g. sulphur. If you have reasonable resolution and you can collect data at a long wavelength from many samples (which has been shown to improve the phasing signals under some

Re: [ccp4bb] visualise xds predicted spots

Dear Tim, It is possible to repurpose some of the DIALS tools to allow this: I will however confess that it is *not obvious* at first glance. Example follows where I ran XDS in ../integrate (i.e. within xia2 as it happens, though this is not relevant here) if you happen to have a relatively

Re: [ccp4bb] xia2 in CCP4 7.0 not seeing files

Dear Andreas We (the xia2 & CCP4 core team) intend to put some effort into improving the i2 gui for xia2 over the next couple of months – this shows that there are two gaps – - it is not clear what the input is – it really should be - you should be able to specify images /

Re: [ccp4bb] Spacegroups, screw axes and ordering

relevant IUCr committees on conventions have on our >>> behalf), why you then want to go and do something completely different? >>> >>> Cheers >>> >>> -- Ian >>> >>> >>> >>> On 29 January 2016 at 09:30, Kay Die

Re: [ccp4bb] Excluding frames in XDS

Dear Mohamed What I would do is to index with the whole set then process the first 1200 frames with one DATA_RANGE= command and the last 200 in a different directory with a different DATA_RANGE= command (but otherwise similar script) and then combine the two sets with XSCALE. There may be

Re: [ccp4bb] questionable structures

Dear Jacob This is an interesting prospect - in effect you are suggesting (not unreasonably, perhaps?) that PDB-REDO is more reliable as a reviewer than the reviewers, under some circumstances. Possibly the approach I would take with this one would be to highlight that PDB-REDO or other

Re: [ccp4bb] Strange pattern of missing reflections

Easiest thing to do is plot the detx and dety positions and see if the missing ones form a nice pattern of tile joins. Two pounds gets you one they will. If you have a multi axis gonio two sweeps good. If not deliberately misaligned xtal and 180 or more degrees a good thing. In real life the

Re: [ccp4bb] Eigers, and local CBF formats

viewers or tools - > if they can't read HDF5 datasets directly. > > Please let us know if there are inconsistencies or issues. This > invitation extends to all users of this HDF5 capability in autoPROC. > > > With best wishes, > > Clemens, Claus and Gerard. > >

[ccp4bb] DIALS 1.3 release / xia2 0.5

Dear CCP4BB The DIALS team have now released DIALS 1.3 / xia2 0.5: this includes a number of fixes to problems reported over the last couple of months (detailed in release notes) as well as useful developments, particularly for Eiger detector data processing & small molecule data processing.

Re: [ccp4bb] weak low resolution data with high R and good CC1/2

Dear Gergo If you have high multiplicity I would recommend you ignore Rmerge and Rmeas and instead focus on Rpim which tells you the precision of the average data http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors If this *increases* as you add more data then adding the data

Re: [ccp4bb] cbf reading

Dear Clement DIALS is one of the packages which supports reading of and processing of Eiger HDF5 data, and is available from http://dials.diamond.ac.uk/ (dials.image_viewer is the tool you want here) Any problems please don’t hesitate to contact

Re: [ccp4bb] AW: [ccp4bb] Rfree stuck at around 39 %

Dear Mohamed If you're in doubt of the solution you can always process the data in P1 with the unit cell from aP below Since you have used xia2; xia2 space_group=P2 or P1 will reprocess the data with the corresponding space group Solving like that should be "right" just harder (perhaps) than

Re: [ccp4bb] RMSD plot

Dear Madhu I think LSQKAB does what you want http://www.ccp4.ac.uk/html/lsqkab.html (at least, from the description you gave) Best wishes Graeme From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Madhuranayaki Thulasingam Sent: 01 February 2017 10:25 To: ccp4bb Subject:

Re: [ccp4bb] different resolution cutoffs for integration and scaling

Dear Jorge As a rule of thumb I would always integrate every reflection on the detector face & only limit the resolution in scaling (*1) - most integration programs are well behaved when it comes to modelling reflection profiles & integrating spots which are “invisible” As to why you observe

Re: [ccp4bb] XDS questions

Dear All, I agree with Tim - what I was getting at was to perform the scaling exactly once - i.e. with AIMLESS or XDS CORRECT but not both The behaviour Tim describes below is exactly what xia2 does :) Best wishes Graeme -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] XDS questions

Dear Nishant Your statistics will be better taking XDS_ASCII because the scaling has been performed twice i.e. you have had two goes (with different models) of reducing the differences between reflections. This will *always* make the R factors etc smaller – whether the data are better or more

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Dear Eugene Yes this is just indexing and refinement Clearly the documentation needed to be more explicit Best wishes Graeme On 10 Dec 2016, at 17:21, Eugene Osipov > wrote: Dear RIchard, It is probably my problems with understanding. >From

[ccp4bb] Correct reading of HDF5 (meta)data

Dear All, There has been much discussion of XDS efficiently reading HDF5 data - this is of course highly desirable though not sufficient for the correct processing of the data. One thing which I think could very much help the community would be to have data published from beamlines where

Re: [ccp4bb] Fine Phi Slicing

Jacob If you have a complete 360 deg data set and your sample is still alive, and you have a multi-axis gonio, I would recommend rotating the crystal about the beam (ideally by ~ maximum scattering 2-theta angle) and collecting again. This would record your blind region as well as moving the

Re: [ccp4bb] Fine Phi Slicing

James, On On 20 Jul 2017, at 19:06, James Holton > wrote: In my experience you need at least an average of 1 photon/pixel/image before even the best data processing algorithms start to fall over. I do not agree… both XDS and

Re: [ccp4bb] Rmergicide Through Programming

Jacob Rmerge does contain information which complements the others. I'd prefer it remains but agree it needs to be properly understood alongside the others you mention Cheers Graeme On 4 Jul 2017, at 12:00, Keller, Jacob > wrote:

Re: [ccp4bb] Rmergicide Through Programming

HI Jacob Unbiased estimate of the true unmerged I/sig(I) of your data (I find this particularly useful at low resolution) i.e. if your inner shell Rmerge is 10% your data agree very poorly; if 2% says your data agree very well provided you have sensible multiplicity… obviously depends on

Re: [ccp4bb] Rmergicide Through Programming

HI Jacob Yes, I got this - and I appreciate the benefit of Rmeas for dealing with measuring agreement for small-multiplicity observations. Having this *as well* is very useful and I agree Rmeas / Rpim / CC-half should be the primary “quality” statistics. However, you asked if there is any

[ccp4bb] REBATCH error mystery

Afternoon all, Technical harking back to the 90’s FORTRAN CCP4 question if I may I have an MTZ file which has no spots on first couple of images, so the batch headers at the start exist but there are no BATCH values which correspond to these in the actual reflection data I have been bashing

Re: [ccp4bb] REBATCH error mystery

ink > > Latest latest Pointless (prerelease update 043, version 1.11.3) removes batch > headers for leading or trailing batch numbers which are not present in the > reflection list (for you, Graeme) > > > > >> On 6 Jul 2017, at 15:04, Graeme Winter <g

Re: [ccp4bb] Rmergicide Through Programming

istics that come from POINTLESS (excellent though that program is!). Andrew On 5 Jul 2017, at 05:44, Graeme Winter <graeme.win...@gmail.com<mailto:graeme.win...@gmail.com>> wrote: HI Jacob Yes, I got this - and I appreciate the benefit of Rmeas for dealing with measuring agre

Re: [ccp4bb] Rmergicide Through Programming

t; >> On 05/07/2017 09:43, Andrew Leslie wrote: >> >> I would like to support Graeme in his wish to retain Rmerge in Table 1, >> essentially for exactly the same reasons. >> >> I also strongly support Francis Reyes comment about the usefulness of Rmerge >> a

[ccp4bb] DIALS 1.5.1 released

Dear All, DIALS 1.5.1 for synchrotron data has been released - full release notes at https://github.com/dials/dials/releases/tag/v1.5.0 The software may be downloaded from http://dials.github.io/installation.html http://dials.diamond.ac.uk/installation.html

[ccp4bb] "reset" a structure before re-refinement

Dear All, Is there a protocol out there to gently perturb atomic positions so that re-running refinement can essentially put them back without bias from the original refinement? In particular, if trying to perform the Karplus and Diederichs paired refinement protocol, I do not want to run the

Re: [ccp4bb] "reset" a structure before re-refinement

ry SPACEGROUP > shakemodel [ bexclude B1 ] [ breset B1 B2 ] [ randomise X ] [ shift X Y Z ] > end > > > On 17/08/2017 17:17, Graeme Winter wrote: >> Dear All, >> >> Is there a protocol out there to gently perturb atomic positions so that >> re-running refin

Re: [ccp4bb] Optimising data processing of a I432 dataset with 75% solvent content.

Hi Michael What integration program did you use? Different programs can sometimes give rather different results with very weak data. I'd try everything to see if one is better than the others. It's also worth making sure you are up to date. Certainly there are recent changes in xds and dials

Re: [ccp4bb] HKL to mtz

pointless -c xdsin XDS_ASCII.HKL hklout xds_ascii.mtz aimless hklin xds_ascii.mtz hklout merged.mtz << eof scales unity eof should do it - is how I usually do this & it also gives a nice merging report... Best wishes Graeme From: CCP4 bulletin board

Re: [ccp4bb] Data acquisition (MX) positions at Diamond Light Source

[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graeme Winter Sent: 10 November 2017 07:17 To: ccp4bb <ccp4bb@jiscmail.ac.uk> Subject: [ccp4bb] Data acquisition (MX) positions at Diamond Light Source Dear All, We have software engineer posts open at the moment at Diamond Light Source in the M

Re: [ccp4bb] new ContaMiner features

Dear All, As someone who is both a user of external software and supports internally developed software to external users, I am quite familiar with both sides of this argument. From time to time someone will notice a "weird feature" in software - sometimes this is a bug, sometimes misuse

[ccp4bb] Crystallography methods development post at Diamond Light Source

Good morning all, We are looking for an enthusiastic methods developer to join the team here at Diamond developing integration methods for small molecule X-ray diffraction data: http://www.diamond.ac.uk/Careers/Vacancies/All/132_17_CH.html The focus of this work is the analysis of more

Re: [ccp4bb] cannot read h5 data file

Dear Shijun How did you convert? If H5ToXDS it throws away all header information - this tool will preserve the metadata: https://github.com/biochem-fan/eiger2cbf which should allow XDSGUI to work. If DIALS can read the data but comes out with the wrong answer, please could you provide some

[ccp4bb] Data acquisition (MX) positions at Diamond Light Source

Dear All, We have software engineer posts open at the moment at Diamond Light Source in the MX data acquisition team (i.e. beamline user software) - details at http://www.diamond.ac.uk/Careers/Vacancies/All/119_17_CH.html It's an exiting time at the moment, with new beamlines being built,

[ccp4bb] mtzdmp gives segmentation fault

Folks I have a data set with 50 wavelengths in - mtzdmp dies as follows: mtzdmp /dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz ###

Re: [ccp4bb] mtzdmp gives segmentation fault

Sorry all this was obviously meant for the helpdesk... Best wishes Graeme From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Graeme Winter [graeme.win...@diamond.ac.uk] Sent: 26 October 2017 14:56 To: ccp4bb Subject: [ccp4bb] mtzdmp gives

Re: [ccp4bb] "Atomic resolution"

Hi Jacob If there’s fresh air between atoms in coot and you can assign the element by eye it’s atomic resolution to me Probably corresponds to about 1.2A or thereabouts I do however also respect the 0.8A limit used by our chemical crystallography colleagues My two cents... Best wishes

Re: [ccp4bb] Resolution cut off

The most useful information for this can come from paired refinement, which will tell you if the data in outer shell is improving the model. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/ For example On balance it’s unlikely throwing away measurements will make your model better...

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