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...

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] 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] 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] 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

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

[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,

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

[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] 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] "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

[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] 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] 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] 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

[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] 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

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

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

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

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] 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

[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] 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] 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] 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] 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

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

[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] 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] 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. > >

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] 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] 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] 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] 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] on mtz labels

Dear Smith F is some structure factor amplitude, probably half of a map coefficient. Fobs is presumably related to some intensity observation. Important point though: you can name the columns in an MTZ *whatever you like* i.e. F1, F2, F_Hg, … so beyond some conventions adopted by CCP4 programs

Re: [ccp4bb] A polite reminder to xia2 users

in model refinement" Skubak P, Murshudov GN, Pannu NS. Acta Cryst. 2004 D60: 2196-2201 "REFMAC5 dictionary: organisation of prior chemical knowledge and guidelines for its use." Vagin, AA, Steiner, RS, Lebedev, AA, Potterton, L, McNicholas, S, Long, F and Murshudov, GN. Acta Cryst. 2004 D60: 2

Re: [ccp4bb] File systems, data storage and integrity, and "bitrot"

of the better ways through which we can ensure preservation (or at least another backup) of our most important diffraction images? - Ally ps I should also say that I originally learned of Zenodo from Graeme Winter at Diamond. - Allister Crow Department of Pathology University o

Re: [ccp4bb] a question related to structurebiology publication

From: http://www.ccp4.ac.uk/ccp4bb.php “CCP4bb is an electronic mailing list intended to host discussions about topics of general interest to macromolecular crystallographers. Any crystallographic-related item is acceptable, and doesn't have to be directly related to CCP4. The bulletin board

Re: [ccp4bb] reading and querying MTZ files

Dear Wolfram For “I was looking for a well-defined, stable interface for scripting in python“ You can do much worse than using cctbx i.e. >>> from iotbx import mtz >>> m = mtz.object('scaled.mtz') (then play with m i.e. help(m) to discover capabilities) – I use this all over the place in

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] 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] 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] imosflm errors

Dear Ivan This is not a xia2 error, rather something very unhappy with ccp4i - you should be getting this error from almost any ccp4i session? I expect more ccp4i expert people will be able to help here. It is also possible (indeed, easier) to run xia2 from the command line, for more

Re: [ccp4bb] How many is too many free reflections?

is not relevant, percentage is. Approximate consensus (i.e. what I will look at doing in xia2) - probably follow Randy Read recipe from ccp4wiki as this seems to (probably) satisfy most of the criteria raised by everyone else. On Tue, Jun 2, 2015 at 11:26 AM Graeme

[ccp4bb] How many is too many free reflections?

Hi Folks Had a vague comment handed my way that xia2 assigns too many free reflections - I have a feeling that by default it makes a free set of 5% which was OK back in the day (like I/sig(I) = 2 was OK) but maybe seems excessive now. This was particularly in the case of high resolution data

Re: [ccp4bb] Point group

Dear Mohamed You can get the equivalent of frame.CBF by using the duals image viewer with datablock or experiments.json and integrated.pickle. this will allow you to step through the frames looking at the actual integration boxes. Best wishes Graeme On 21 May 2015 17:02, Mohamed Noor

Re: [ccp4bb] XDS INP

Dear All, Starting from here I would just use the generate_XDS.INP script developed by Kay Diederichs: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP It will make the necessary input files from just the image headers. best wishes Graeme On Thu, May 7, 2015 at

Re: [ccp4bb] XDSCONV not using a keyword?

Hi Nathan, While what you observe does sound like a bug I would not like to comment whether this is right or wrong. However a CCP4 alternative to this which I find easier to use is pointless - pointless -c xdsin XDS_ASCII.HKL hklout sorted.mtz This will give an unmerged MTZ which can be used in

Re: [ccp4bb] PAD images

Looking at PAD images is something we have had to get used to at Diamond, and sometimes it takes some tweaking to get a really good idea of what the images actually look like. This is a challenge if you measure the data properly with fine slicing low dose... One thing which really helps is to

[ccp4bb] DIALS Workshop at ECM 29

you there! Best wishes, Graeme Winter, David Waterman Gwyndaf Evans When? August 23rd, 2015 (Sunday), 10:00 AM – 3:30 PM Where? Rovinj (Red Island), Hotel “Istra”, Huetterot congress hall Registration fee: EUR 20,00 (Registration through the registration system of the ECM29). Number

Re: [ccp4bb] Continuous-Single Versus Coarse-Multiple Sampling

Dear Jacob, There are a multitude of directions you can go from here - a few comments spring to mind: - are repeated observations of the same reflection on the same part of the detector really independent? - for the wide phi sliced vs. fine sliced discussion the detector type matters a great

Re: [ccp4bb] how to dump diffraction image header info?

Dear All, dxtbx.print_header /path/to/image should work Graemes-MacBook-Pro:~ graeme$ dxtbx.print_header data/i04-BAG-training/th_8_2_0001.cbf === data/i04-BAG-training/th_8_2_0001.cbf === Using header reader: FormatCBFMiniPilatusDLS6MSN100 Beam: wavelength: 0.97625 sample to source

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

)252-0667 rsanishv...@anl.gov -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Graeme Winter [graeme.win...@gmail.com] *Sent:* Thursday, November 13, 2014 2:15 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] To scale or not to scale

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

of the home source ones. See docs. You can specify explicitly I think Phil Sent from my iPhone On 17 Nov 2014, at 09:44, Graeme Winter graeme.win...@gmail.com wrote: Dear Nukri, The following is my opinion which I think is worth discussion, and are based on my understanding of what XDS does

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

Dear Kay Just to comment on (e) since you say you don't know why anyone would want to do this, yet this is exactly what xia2 -3d does :o) I use AIMLESS to merge data already scaled by XDS CORRECT or XSCALE as a way to get a report on the merging statistics which includes all of the AIMLESS

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

the misunderstanding spreads, which is then why I get asked can CORRECT scale a data set? and other misunderstandings along these lines ... best, Kay On Thu, 13 Nov 2014 08:15:12 +, Graeme Winter graeme.win...@gmail.com wrote: Dear Kay Just to comment on (e) since you say you don't know why

Re: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

Dear Jurgen, Thanks for your interest in DIALS - we are working hard at the moment on testing the software and finding bugs (and fixing them!) and I would say right now it's not quite ready for the general user, but we do plan to make an alpha release of the software before the end of the year.

[ccp4bb] Publishing raw data

Hi Folks, Colleague of mine here at Diamond just pointed out a neat EU funded way of publishing raw data which generates a digital object identifier as part of the process: http://zenodo.org Worked through it myself to see if it works and apparently it does: doi:10.5281/zenodo.10271 Thought

Re: [ccp4bb] Xia2 / XDS issues

Dear Tony, OK, clearly Tim's suggestion is spot on, to remove the offending images from processing (this is easily done by splitting your input xinfo or the automatically generated one, I will copy an example below) I suspect that the memory error results from IMAGE IER SCALE NBKG NOVL

Re: [ccp4bb] Xia2 / XDS issues

Dear Tony, Sorry to hear you are having trouble - I have never seen this message before. Please could you send me (off list) the output of the last XDS job ran before this one and (ideally) the XDS.INP file in the offending area? There must be something very odd going on here. Thanks best

Re: [ccp4bb] Pilatus and Strategy wrt Radiation Damage

Hi All, A major opportunity with Pilatus detectors is the chance to redistribute the dose in reciprocal space i.e. measure a lot more data, with less dose / frame, then decide in hindsight where you probably should have cut off the data set. It is certainly true that strategies such as 0.2 s/0.2

Re: [ccp4bb] Pilatus and Strategy wrt Radiation Damage

signal-to-noise and to turn your sentence you may get better data into you will get better data. I think this would be worth implementing at beamlines - do you know if anything in this direction is on its way? Best, Tim On 05/01/2014 09:25 AM, Graeme Winter wrote: Hi All, A major

[ccp4bb] Observed criterion sigma(I|F)

Hi Folks, A xia2 user wrote in asking where to find 'observed criterion sigma(F)' and 'observed criterion sigma(I)' in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea what they are so will struggle to give a helpful answer ;o) and surprisingly google was not a lot of use

Re: [ccp4bb] Observed criterion sigma(I|F)

what Scala does. On 25 Nov 2013, at 09:21, Graeme Winter graeme.win...@gmail.com wrote: Hi Folks, A xia2 user wrote in asking where to find 'observed criterion sigma(F)' and 'observed criterion sigma(I)' in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea what

Re: [ccp4bb] 100% Rmerge in high resolution shell

Usually this means that you have relatively high multiplicity, which give-or-take improves the I/sig(I) by sqrt(m) where m is the multiplicity, but also increases the Rmerge. For any given narrow shell of reflections, Rmerge ~ 0.8 / unmerged(I/sig(I)) merged(I/sig(I)) ~ sqrt(m) *

Re: [ccp4bb] strange unit cell

You could try putting this into the Zanuda server http://www.ysbl.york.ac.uk/YSBLPrograms/ which will search for possible correct spacegroups given the coordinates and structure factors. There are however no reasons why you can't have a pseudo-cubic monoclinic lattice, however unlikely it is.

[ccp4bb] Post-doctoral position at Diamond Light Source in Experimental Phasing

integration software. For further information please contact Graeme Winter ( graeme.win...@diamond.ac.uk) or Dave Hall (david.h...@diamond.ac.uk) though for applications please use the link above. The closing date is the end of September. Best wishes, Graeme and Dave

[ccp4bb] Fwd: [ccp4bb] is there any version of xia2 or XDSME compatible with new XDS?

Dear Rain Field, A new xia2 release is now available please see: http://xia2.blogspot.com for details. This version should be included in the next CCP4 update. Once again apologies for the inconvenience. Best wishes, Graeme On 4 July 2013 08:18, Graeme Winter graeme.win...@gmail.com wrote

Re: [ccp4bb] is there any version of xia2 or XDSME compatible with new XDS?

Dear Rain Field, The current release is indeed unable to work with the newest versions of XDS and a new version should be available before the end of the week, which will be advertised on the blog. However this requires either a new nightly build of phenix or an unreleased cctbx build, as bits of

Re: [ccp4bb] PILATUS data collection

A couple of extra comments on top of Bob's rather comprehensive recommendations, based purely on actually looking at Pilatus data (I mean *looking*) When you are inspecting the images looking at them at 100% size is important: spots are small relative to pixels and the point spread is essentially

Re: [ccp4bb] Why the name aimless

Suspect most people would be looking for painless though I would guess that should be a program to tell you the right crystallization conditions... On 3 May 2013 00:15, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Nevertheless? JPK On Thu, May 2, 2013 at 2:18 PM, Roger Rowlett

Re: [ccp4bb] How to calculate data collection strategy manually?

Dear Saleem, To compute one manually I take it you mean by hand with commonly available software as opposed to via e.g. automated beamline methods? If so: start up imosflm index your image(s) and estimate mosaic spread select strategy, auto-complete, go XDS has XPLAN equivalently, though you

Re: [ccp4bb] Diffraction image compression

Dear Eugene, Personally I have a habit of using bzip2 for archival of data. Negative points: very slow. Positive points: universally supported, lossless. I have lots of data. To be honest most of it I keep in the native format. I expect to see plenty of comments of lossless vs. lossy compression

Re: [ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert

Hi Folks, To follow up Harry's comments. We have a Pilatus 300K on I19 here at Diamond which is used from time to time for small molecule work. Processing with XDS has proved to be successful (I can send an example XDS.INP but you will need to make sure you have a good knowledge of the

Re: [ccp4bb] statistics from a structure factors file

Hi Sebastiano, If they hand you an *unmerged* mtz file containing scaled data you can do this, by remerging the data with Scala or Aimless. Equivalently the unmerged output of scalepack or XSCALE (or XDS CORRECT) If however you have merged data then you have lost this information, though

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

The XDS CORRECT step will also (by default) do scaling - if I understand correctly the same scaling as in XSCALE, but for a single sweep and with no zero-dose. If what you want is merging statistics, I find it helpful to write out the data unmerged and then use pointless -c and aimless to merge

Re: [ccp4bb] Copying R-free flags - possibly daft question.

Dear All, Sorry, finally have released an updated version where this problem has gone away: xia2.blogspot.com has the details. Best wishes, Graeme On 6 November 2012 10:31, Graeme Winter graeme.win...@gmail.com wrote: Well there's a funny thing. It seems that this is already in xia2

Re: [ccp4bb] Copying R-free flags - possibly daft question.

. best wishes, Graeme On 5 Nov 2012, at 15:13, Graeme Winter wrote: Thanks indeed Eleanor, when I get a moment I will add this too to the xia2 cad script! Best wishes, Graeme On 5 November 2012 11:37, Antony Oliver antony.oli...@sussex.ac.uk wrote: Thanks Eleanor - guess I should

Re: [ccp4bb] Copying R-free flags - possibly daft question.

Hi Antony, Using xia2 with a reference dataset for both indexing and R-free seems to work fine, apart from the fact that the resulting mtz file, now contains R-free labels for reflections that have no observations… i.e. taken from the higher resolution reference dataset; see output below.

Re: [ccp4bb] Copying R-free flags - possibly daft question.

Thanks indeed Eleanor, when I get a moment I will add this too to the xia2 cad script! Best wishes, Graeme On 5 November 2012 11:37, Antony Oliver antony.oli...@sussex.ac.uk wrote: Thanks Eleanor - guess I should have plumbed the depths of the CAD manual a little further. Works perfectly.

Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?

Hi Phil, Usually with something like this I use: Data line--- bins 20 Data line--- resolution 2.80 Data line--- run 1 batch 1 to 900 Data line--- resolution run 1 high 2.80 Data line--- name run 1 project AUTOMATIC crystal DEFAULT dataset SAD Data line--- scales constant Data

Re: [ccp4bb] zero mosaicity

Hi Ed, If you use XDS for integration then all of the reflections are full (they are summed by the program during the integration), so there are no partials from which to determine an estimate of the mosaic spread in Scala. Mosflm 0 mosaic spread is a different issue, but has been much improved

Re: [ccp4bb] Image names

in questions_answers: answer = template_regex(filename) assert answer[0] == questions_answers[filename] On 30 April 2012 09:19, Graeme Winter graeme.win...@gmail.com wrote: Hi Folks, Following some bug reports I spent a few minutes over the weekend wrangling with regular

[ccp4bb] Image names

Hi Folks, Following some bug reports I spent a few minutes over the weekend wrangling with regular expressions to digest image file names - the dismantling of e.g. foo_bar_001.img to foo_bar_###.img, 1 etc. I think now that the scheme I have should work for everything, however what I could

Re: [ccp4bb] Trying to cut the resolution of the datasets

detector area and the outer parts contain only noise, the noise has a negative effect on the real data. Tim On 03/19/12 15:25, Graeme Winter wrote: ... presuming of course the automated software got this resolution limit right. If for whatever reason you would like to cut the limit mtzutils

Re: [ccp4bb] Trying to cut the resolution of the datasets

... presuming of course the automated software got this resolution limit right. If for whatever reason you would like to cut the limit mtzutils will do this nicely: mtzutils hklin blah_free.mtz hklout blah_lower.mtz eof resolution 1.8 eof (say) - I am sure there are other ways within the suite

Re: [ccp4bb] Trying to cut the resolution of the datasets

of your data e.g. with pointless (I/sigI 2.0 is a good marker) and reprocess the data to that limit. If you integrate the whole detector area and the outer parts contain only noise, the noise has a negative effect on the real data. Tim On 03/19/12 15:25, Graeme Winter wrote: ... presuming

Re: [ccp4bb] mosflm and pilatus 2M

Mosflm works fine with our Pilatus 2M at DLS - however you do need to be using the beta-test version. http://www.mrc-lmb.cam.ac.uk/harry/mosflm/betas/ best wishes, Graeme On 12 March 2012 19:57, Dean Derbyshire dean.derbysh...@medivir.com wrote: Hi again, it's the 2M  detector I'm having

Re: [ccp4bb] merge dataset

Hello Deng, Process them as usual with e.g. Mosflm, then sort them together (you may need to rebatch one of the runs) and do one Scala run - this will put all of the measurement on a common scale and write out data suitable for refinement. For pointgroups with ambiguous origin choices (e.g. P4)

Re: [ccp4bb] question about input .hkl file for SHELXD

Hello Lu, I would usually suggest using mtz2sca (f you have an MTZ with intensities) to get a scalepack format file, which you may have already. Then I would use shelxc to generate the .ins and .hkl file for shelxd. You can do this through ccp4i from an MTZ file, or write a script as detailed

Re: [ccp4bb] Opinion on automation

Dear Theresa, My answer would be - it depends. If you are in the business of learning crystallography, then I would absolutely suggest you start from doing everything by hand. Indeed, if you really want to get stuck in I would suggest starting with the programs you need (mosflm, scala, truncate

Re: [ccp4bb] xia2 error

Dear Steve, Thanks for getting in touch. It seems that for some reason the ccp4i interface to xia2 is not currently working correctly. I will look into this and get back to you with a fix, it currently has me confused. Best wishes, Graeme On 17 February 2012 12:54, Stephen Carr

Re: [ccp4bb] xia2 error

On 17 February 2012 15:44, Graeme Winter graeme.win...@gmail.com wrote: Dear Steve, Thanks for getting in touch. It seems that for some reason the ccp4i interface to xia2 is not currently working correctly. I will look into this and get back to you with a fix, it currently has me confused. Best

Re: [ccp4bb] Merging hi and low res data

Dear Nick, If you're happy to keep on using xia2, you can just put both of the data sets in a single directory and run xia2 -3dii /heres/where/the/data/went And wait a little while. To comment on your analysis of the statistics: inside xia2 the scaling is switched off as far as possible in the

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