Re: [ccp4bb] xds crashes

Dear Kay, many thanks for your suggestions. We will look into this. best Demetres On 11/29/2022 2:35 PM, Kay Diederichs wrote: Dear Demetres, I googled the Ubuntu 22.04 release notes and found https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 which says "We’ve enabled the

Re: [ccp4bb] xds crashes

Dear Demetres, I googled the Ubuntu 22.04 release notes and found https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 which says "We’ve enabled the userspace OOMD service and are shipping the systemd-oomd package by default on the “Ubuntu Desktop” flavour, to avoid overloaded sys

Re: [ccp4bb] xds crashes

Dear Demetres, On Tue, Nov 29, 2022 at 10:25:17AM +0200, Demetres D. Leonidas wrote: > Dear Kay, > > you are right and I do apologize for the misunderstanding. Point 1 > and 2 are sufficient. You can probably avoid doing any of this by using the LIB= feature of XDS on gzipped CBF files with the

Re: [ccp4bb] xds crashes

Dear Kay, you are right and I do apologize for the misunderstanding. Point 1 and 2 are sufficient. best Demetres On 11/29/2022 10:00 AM, Kay Diederichs wrote: Dear Demetres, sounds a bit drastic! The second point alone would certainly suffice, because then no forking is done. What kind of

Re: [ccp4bb] xds crashes

Dear Demetres, sounds a bit drastic! The second point alone would certainly suffice, because then no forking is done. What kind of hardware is that? I would expect that on a contemporary workstation you have 8GB of RAM or more; that would allow for 8 or more processes. Do you have a swapfile? If

[ccp4bb] MhRe: [ccp4bb] xds crashes

marc-requ...@jiscmail.ac.uk> Sent: Tuesday, November 29, 2022 6:34:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] xds crashes Dear Kay, after some digging and help from Max Nanao we found that the problem was the memory. It was fulling rapidly. The workaround was to: 1. unzip the cbf fi

Re: [ccp4bb] xds crashes

Dear Kay, after some digging and help from Max Nanao we found that the problem  was the memory.  It was fulling rapidly. The workaround was to: 1. unzip the cbf files prior to processing 2. use maximum number of jobs 1 3. use number of processors 4 4. run xds_par Many thanks for all your h

Re: [ccp4bb] xds crashes

Dear Demetres, I agree with what James says: this is the operating system trying to to prevent, in an over-zealous way, the forking of too many or too big (in terms of memory) processes. In other words, XDS hasn't changed, but the operating system changed - it applies different limits to its pr

Re: [ccp4bb] xds crashes

Sounds like your kernel might think "forkxds" is creating a "fork bomb".  Too many sub-processes firing off in too short a time triggers this.  On one of my systems, I fixed it by editing /etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more pids than normal.  This tends to p

[ccp4bb] xds crashes

Dear all, I do not know if this is the right list and I would like to apologize if it is not. We have repeatedly experienced xds crashes in machines running ubuntu 22.04.1 with the following message repeated several times at the INTEGRATE step /usr/local/bin/forkxds: line 60:  3427 Done ec

[ccp4bb] XDS package: new version and support for Apple M1

Dear academic users of XDS, there is an updated version available at https://xds.mr.mpg.de/ . Since the old (current) version will expire in March, it is advisable to download and test the updated version before that. The biggest change is the availability of binaries for the Apple M1 processor.

Re: [ccp4bb] [xds] how to specify measuring angle

On 2020-10-09 01:59, Dirk Kostrewa wrote: Dear Doo Nam Kim, On 09.10.20 08:43, Doo Nam Kim wrote: Since I don't know correct value of OSCILLATION_RANGE, I just changed to the example value (0.1) from (0.89976, I know it is not a positive multiple of 0.0001, but worked for ketone data). w

Re: [ccp4bb] [xds] how to specify measuring angle

Hi Doo Nam Kim, If you do not know your OSCILLATION_RANGE, a good guess would be to take your collection angle range (-60 to +60 or 120 degrees) and divide that by the number of frames. Best, Jessica On Fri, Oct 9, 2020 at 2:00 AM Dirk Kostrewa < dirk.kostr...@lrz.uni-muenchen.de> wrote: > Dear

Re: [ccp4bb] [xds] how to specify measuring angle

Dear Doo Nam Kim, On 09.10.20 08:43, Doo Nam Kim wrote: Since I don't know correct value of OSCILLATION_RANGE, I just changed to the example value (0.1) from (0.89976, I know it is not a positive multiple of 0.0001, but worked for ketone data). without knowing the correct value for the O

Re: [ccp4bb] [xds] how to specify measuring angle

Dear Doo Nam Kim, actually the results of XDS processing are deterministic for all practical purposes (to be nitpicking, the multi-processor version xds_par may result in slighly different output each time it is run, because for a few calculations the order of operations is influenced by the o

Re: [ccp4bb] [xds] how to specify measuring angle

Once I turned off my vpn, I could download from https://data.sbgrid.org/dataset/222/ Thank you for your help. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SU

Re: [ccp4bb] [xds] how to specify measuring angle

Thank you Tim and Kay. "the indexing procedure is independent of the starting angle of the first frame." --> I see, since XDS does indexing, I think that XDS is independent of the starting angle of the first frame "Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree per fram

Re: [ccp4bb] [xds] how to specify measuring angle

I agree with Tim that Doo Nam Kim's question appears to be directed towards the rotation per frame, which is specified in XDS.INP using OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!) please see the documentation at http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_

Re: [ccp4bb] [xds] how to specify measuring angle

Dear Doo Nam Kim, the indexing procedure is independent of the starting angle of the first frame. Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree per frame during data collection? Best regards, Tim On Thu, 8 Oct 2020 09:28:07 +0100 Doo Nam Kim <4e720d49e642-dmarc-requ..

[ccp4bb] [xds] how to specify measuring angle

I think that my microED data was measured with -60 to 60 rotation angle. However, STARTING_ANGLE= -60. in my XDS.INP resulted in ... # COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES 1 0.0020349 0.0108237 0.0096964 1.00 -0.00 -0.00 2 -0.0056895-0.0002762

Re: [ccp4bb] XDS Data Processing

Hi Maria, XDSGUI is documented at https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI . The easiest way to learn it is of course if you find somebody to show it to you. Are you the only one in your lab who uses it? If you have a XDS-on-Mac problem, check out the Installation art

Re: [ccp4bb] XDS Data Processing

Hello Maria! I would recommend these 2 links: https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Tutorial(First_Steps) and for difficult datasets: https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Difficult_datasets Are you having problems with the “generate XDS.inp?” Maybe

[ccp4bb] XDS Data Processing

Hello Friends, I am trying to use XDS GUI for data processing in Mac. I am having an error while loading the raw image files. Should I convert them to any specific format? Also is there any good tutorial for the beginners for using the GUI? Thanks in advance.

Re: [ccp4bb] XDS on Windows

Hi Jan, Hi Rob, hi Gustavo, thanks for you answers. I totally missed the thread in the bb and couldn't find anything in the archive also the wiki entry - frankly I havn't checked that one for a while ... Great to know that the CU update solves most of the issues regarding the openMP virt

Re: [ccp4bb] XDS on Windows

Hi Jan, Rob, it is documented in XDSwiki at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Installation#Windows - I just added the hints concerning the Creators Update (can anybody verify that OpenMP parallelization works with that??). best, Kay On Tue, 23 May 2017 14:06:54 +010

Re: [ccp4bb] XDS on Windows

Hi Jan, There were some postings on the bulletin board about this in the latter half of August last year. I also recall problems with the parallel version of XDS but I think this was fixed by Microsoft in a patch that I believe is included in the recent Creators update to Windows 10. Can't ver

Re: [ccp4bb] XDS plugin for efficient reading of HDF5 data

Dear all, unfortunately the very latest BUILT of the XDS package (which fixed a problem in XDSCONV) introduced a last-minute bug in the routine that uses the "Neggia" plugin. This is documented, together with two workarounds, in the Troubleshooting section of the Eiger article in XDSwiki : htt

[ccp4bb] XDS plugin for efficient reading of HDF5 data

Dear all, DECTRIS is proud to announce the release of an HDF5 read plugin to take advantage of the recently added XDS plugin support (thanks to Wolfgang Kabsch and Kay Diederichs) and accelerate the reading of HDF5 files. EIGER detectors produce data in the large-data format HDF5. Despite substan

Re: [ccp4bb] XDS Gui license expired?

Hi Susan, it looks like your XDS license has expired. Download a newer XDS version from http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html Best regards, Karine On 01/09/17 16:33, Susan Kathleen Fetics wrote: Hello, I was trying to open XDS gui in Linux and it would not work. I wa

[ccp4bb] XDS Gui license expired?

Hello, I was trying to open XDS gui in Linux and it would not work. I was given the notice "Sorry, license expired Sept 30, 2016" with no other options as far as I could tell. How can I correct this so XDS gui works again? Thanks in advance, - Susan

Re: [ccp4bb] XDS questions

I had some cases, when path INTEGRATE.HKL -> Aimless gave data, from which it was not possible to solve structure by Phaser. It looked like structure solved, but then I got 45-50% Rwork/free. There were no problems with XDS_ASCCI.HKL -> Aimless (Not scale, just merge) path. Jan On 11/24/2016 0

Re: [ccp4bb] XDS questions

Thanks everyone for your replies. cheers Nishant On Mon, Nov 21, 2016 at 6:03 PM, Wei Wang wrote: > My personal test shows that the different paths vary little with each > other, as long as the scaling is done only once. Another way could be what > is said on XDSwiki: Minimum I/Sigma=50, CORREC

Re: [ccp4bb] XDS questions

Hi, I do this by editor (and cut / paste). Clumsy but works. Let me know if you find a more elegant way. Cheers, Boaz Original message From: Wei Wang Date: 21/11/2016 19:05 (GMT+02:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] XDS questions My personal

Re: [ccp4bb] XDS questions

My personal test shows that the different paths vary little with each other, as long as the scaling is done only once. Another way could be what is said on XDSwiki: Minimum I/Sigma=50, CORRECTIONS=MODULATION, NBATCH=1. Then the XDS_ASCII.HKL is handed over to Aimless with default settings. One que

Re: [ccp4bb] XDS questions

XDS-CORRECT and Aimless use 1. different scaling models - CORRECT includes a poorly documented correction across the detector plane not present in Aimless: this may or may not be a Good Thing 2. different outlier rejection algorithms - XDS seems to reject more observations 3. different “corr

Re: [ccp4bb] XDS questions

@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: 21 November 2016 11:14 To: ccp4bb Subject: Re: [ccp4bb] XDS questions Dear Nishant, XDS_ASCII.HKL contains corrected, scaled, but not merged reflections. You can specifically ask XDS to merge your data, but I would not do so unless really necessary - you

Re: [ccp4bb] XDS questions

Dear Nishant, XDS_ASCII.HKL contains corrected, scaled, but not merged reflections. You can specifically ask XDS to merge your data, but I would not do so unless really necessary - you loose a lot of information. I would like to offer a different opinion to Graeme's: You can read XDS_ASCII.HKL

Re: [ccp4bb] XDS questions

est wishes Graeme From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nishant Varshney Sent: 21 November 2016 10:37 To: ccp4bb Subject: Re: [ccp4bb] XDS questions Dear All, Just to understand more, the XDS_ASCII.HKL file generated after running XDS contains scaled and mer

Re: [ccp4bb] XDS questions

Dear All, Just to understand more, the XDS_ASCII.HKL file generated after running XDS contains scaled and merged reflections? Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS instead of INTEGRATE.HKL file?? I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL

Re: [ccp4bb] XDS questions

Thanks everyone for answering the question! Best, Wei On Thu, Nov 17, 2016 at 4:20 PM, Michael Martynowycz < michael.martynow...@gmail.com> wrote: > Wei, > > You can use the integrated integrated intensities only if you want to go > the ccp4 route. Sort the integrated reflections, then scale an

Re: [ccp4bb] XDS questions

Wei, You can use the integrated integrated intensities only if you want to go the ccp4 route. Sort the integrated reflections, then scale and truncate them using: Pointless xdsin INTEGRATE.HKL hklout sorted.mtz Aimless hklin sorted.mtz hklout scaled.mtz Hope that helps. -Mike Sent from my iP

Re: [ccp4bb] XDS questions

Dear Wei, if you process your data with XDS, the best is probably to do the scaling in XDS (CORRECT) and be done with it. If you want to use Aimless for merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES CONSTANT. All best. Andreas On Thu, Nov 17, 2016 at 9:40 PM, W

Re: [ccp4bb] XDS questions

Wei, The flag MAXIMUM_NUMBER_OF_PROCESSORS= in XDS.INP should allow you to choose the number of processors you wish to use. Cheers, Jim

[ccp4bb] XDS questions

Hi, Is there a way to let xds_par use less than all processors/threads on the machine? Sometimes I would like to process something else while XDS is running. Another question is related to the scaling procedure. My understanding is that the XDS already does the scaling during correction. So if I

Re: [ccp4bb] XDS

. Best wishes Graeme From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of chemocev marker Sent: 14 April 2016 08:49 To: ccp4bb Subject: [ccp4bb] XDS Dear All If some one has a a good tutorial (written or video) for using the XDS. I will be glade to know about it. best Jiri

Re: [ccp4bb] Fwd: [ccp4bb] XDS Rmeas in space group determination

Dear Chen, On Thu, May 14, 2015 at 10:05:05AM -0400, Chen Zhao wrote: > Thanks a lot for your reply! I am a little surprised to learn that the > centrosymmetry is always considered as a point groups symmetry component. > That might explain why all the anomalous data I have seen have higher Rmeas >

[ccp4bb] Fwd: [ccp4bb] XDS Rmeas in space group determination

From: Chen Zhao Date: Thu, May 14, 2015 at 10:04 AM Subject: Re: [ccp4bb] XDS Rmeas in space group determination To: Kay Diederichs Hi Kay, Thanks a lot for your reply! I am a little surprised to learn that the centrosymmetry is always considered as a point groups symmetry component. That

Re: [ccp4bb] XDS Rmeas in space group determination

Hi Chen, if Rmeas is high (like 50 and up) even in P1 then maybe the integration was not right, or the indexing is offset by 1 in h or k or l ? To check the former, look at FRAME.cbf and see if the predictions match the spots. To test the latter try echo CENTRE | pointless XDS_ASCII.HKL best,

[ccp4bb] XDS Rmeas in space group determination

> Hi Ethan, > > Thanks a lot for your detailed information. I am aware that in IDXREF only > the lattice symmetry was tried to be determined. I went back to check the > subtrees in IDXREF because even for P1 the Rmeas is very high, meaning that > the multiple measurements for the same reflectio

Re: [ccp4bb] XDS Rmeas in space group determination

On Wednesday, 13 May, 2015 18:17:04 Chen Zhao wrote: > Hi Ethan, Sorry, I'm coming in late on this so I might have missed an earlier explanation of exactly what programs are involved. > Yes. My question was simply whether it calculates the statistics >

Re: [ccp4bb] XDS Rmeas in space group determination

Hi Ethan, Yes. My question was simply whether it calculates the statistics from completely unmerged intensities and just compare say h,k,l with -h,-k,l (or -h,-k,-l and h,k,-l) if there is a 2-fold? Although I believe so... And what is a good number? Is 20 % OK? What about 30 % and even higher?

Re: [ccp4bb] XDS Rmeas in space group determination

On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote: > Hi all, > > I am sorry about this question which I should have figured out earlier. For > point group determination, does the Rmeas consider Fridel pairs > differently? A Friedel pair consists of the [hkl] and [-h-k-l] reflections. This pairi

[ccp4bb] XDS Rmeas in space group determination

Hi all, I am sorry about this question which I should have figured out earlier. For point group determination, does the Rmeas consider Fridel pairs differently? (although I think it should be...) This is because I saw a derivative dataset collected at peak (from a demo) whose Rmeas is quite high (

Re: [ccp4bb] XDS INP

On Tue, 12 May 2015 17:24:18 -0500, Gerd Rosenbaum wrote: ... >But no big deal. It's a -1 in one of the axes definitions. There are, as >you stated, many more axes definitions and they depend on the geometry >of the end station. E.g., at the SBC, the orientation of otherwise >identical goniostats

Re: [ccp4bb] XDS INP

Dear Natalie, I try to run my images with fast_dp, but got the error message: Fast_DP installed in: /home/lu/bin/fast_dp_20141205 Starting image: /home/lu/Documents/hg6l3/Hg6_L3_1_2.mccd Number of jobs: 1 Number of cores: 0 Processing images: 1 -> 360 Phi range: 112.50 -> 472.50 Template: Hg6

Re: [ccp4bb] XDS INP

Hi Clemens, your suggested description of positive rotation doesn't remove the ambiguity. My intuitive way to define positive rotation (in 1994 or so, when building the SBC) was: Looking onto the sample, rotation of the sample in mathematically positive direction Only later I was told th

Re: [ccp4bb] XDS INP

Hi Kay, On Tue, May 12, 2015 at 08:39:24PM +0100, Kay Diederichs wrote: > According to > http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ROTATION_AXIS= > the definition of a positive value in the ROTATION_AXIS= line is: > > "When looking along the axis, the crystal w

Re: [ccp4bb] XDS INP

According to http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ROTATION_AXIS= the definition of a positive value in the ROTATION_AXIS= line is: "When looking along the axis, the crystal would rotate clockwise when proceeding to the next data image." There is of cour

Re: [ccp4bb] XDS INP

Hi As far as I am aware beamline BL17U at Shanghai has what we in the Mosflm world call "reverse phi" (or in the XDS world you'd want to change the ROTATION AXIS vector). There are often good reasons (to the engineers who have installed the equipment on the beamline) why the crystal rotation i

Re: [ccp4bb] XDS INP

I not so familiar with data collection hardware! I still have a lot to learn. This data set was collected from SSRF(Shanghai China). I don't know how they rotate the spindle. Can you provide me some reference material？ Best wishes! -- 卢作焜 南开大学新生物站A202 At 2015-05-12 22:41:24, "Kay Dieder

Re: [ccp4bb] XDS INP

Yes! two data sets from one crystal with 2 different wave length. -- 卢作焜 南开大学新生物站A202 在 2015-05-12 22:14:16，"Huw Jenkins" 写道： >Hi, > >Also the IXDREF.LP files from yesterday and today suggest that you are having >problems with 2 different datasets. Is that correct? > >IDXREF from yesterda

Re: [ccp4bb] XDS INP

You found it! XDS.INP needs ROTATION_AXIS=-1 0 0 with this setting, IDXREF indexes more than half of the reflections: REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 10956 INDEXED SPOTS REFINED PARAMETERS: AXIS BEAM ORIENTATION CELL STANDARD DEVIATION OF SPOTPOSITION (PIXELS)

Re: [ccp4bb] XDS INP

Hi, Also the IXDREF.LP files from yesterday and today suggest that you are having problems with 2 different datasets. Is that correct? IDXREF from yesterday had: NAME_TEMPLATE_OF_DATA_FRAMES=/home/lu/Documents/StructurePro/images/luzk/Hg6/hg6_L1_1_? OSCILLATION_RANGE=0.5000 X-RAY_WAVELE

Re: [ccp4bb] XDS INP

On 12 May 2015, at 13:09, luzuok wrote: > STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 11.13 Is the oscillation range and rotation axis direction correct in your XDS.INP file? Huw

Re: [ccp4bb] XDS INP

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Natalie, I usually look at the first frame with adxv and estimate the ORGX ORGY (which can be different from the direct beam position) by eye based on shadows (as Kay mentioned before) or ice rings and copy the values into XDS.INP. Regards, Tim

Re: [ccp4bb] XDS INP

Dear Natalie, On Tue, May 12, 2015 at 02:08:42PM +0100, Natalie Tatum wrote: > Dear Lu, > > Just last week I faced an almost identical problem: iMoslfm had no problem > but XDS failed. Yes - that happens often because the beam centre recorded in the image header doesn't specify what coordinate s

Re: [ccp4bb] XDS INP

Dear Lu, Just last week I faced an almost identical problem: iMoslfm had no problem but XDS failed. I discovered, as Kay has suggested, the ORGX and ORGY values were incorrect in XDS.INP. In fact, they had essentially been swapped. If you have AUTOINDEX.INP from fast_dp, you can compare the values

Re: [ccp4bb] XDS INP

Dear LU, yes, your spot_15.png looks good. What worries me now is the table INDEX_ QUALITY DELTAXD YD X Y Z DH DK DL ORIGIN 0 0 0 1.70.1997.7 1020.9 0.0010 0.0005 1.02190.38 0.510.25 0 -1 0 3.00.4

Re: [ccp4bb] XDS INP

Dear Kay, I've tune these parameter for many times, and I got best results . : SPOT_RANGE=1 100 INCLUDE_RESOLUTION_RANGE=50 4.2 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=20 but still got the same error message! The SPOT.XDS file was ploted (see attachment "spot_15.png" ), it seems that t

[ccp4bb] AW: [ccp4bb] XDS INP

you could do. You may even process with Mosflm and see what comes out here. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jurgen Bosch Gesendet: Montag, 11. Mai 2015 15:57 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] XDS INP Edit your XDS.INP file to

Re: [ccp4bb] XDS INP

Hi LU, the reason why IDXREF is not indexing smoothly is that the spot positions in your SPOT.XDS are not very meaningful - you pick up a lot of noise! I plotted your SPOT.XDS using %%:-/tmp/luo% gnuplot gnuplot> set size square gnuplot> set out "tmp.png" gnuplot> set term png nocrop medium si

Re: [ccp4bb] XDS INP

Edit your XDS.INP file to look like this: !JOB= XYCORR INIT COLSPOT IDXREF JOB=DEFPIX INTEGRATE CORRECT Then rerun ads and be happy thereafter. and RTFM ! Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular

Re: [ccp4bb] XDS INP

Hi Lu Mosflm indexes your image using all defaults without any problems ;-) XDS shouldn't have any difficulties with indexing this. I suspect your crystal only diffracts to ~3.0 - 3.5 Å so you could do a better experiment by moving the detector back to ~ 900mm... BUT - PLEASE don't attach your

Re: [ccp4bb] XDS INP

The process failed. You mean it didn’t process the data past the indexing routine? That just means you need to actually change some values and type in a couple of commands into XDS.INP - not everything can be designed to be point & click. Look at IDXREF.LP and check out what the suggested space g

Re: [ccp4bb] XDS INP

Dear all, Thank you for all your excellent suggestions! The XDS package now works smoothly in xdsapp in my Linux. Unfortunately, due to the data quality or maybe my ability, the process was failed. Best wishes! Lu Zuokun -- 卢作焜 南开大学新生物站A202 At 2015-05-08 03:39:07, "Clemens Vonrh

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 11:34

Re: [ccp4bb] XDS INP

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Lu, according to the file ending (mccd) in the def-file, you collected data with a MAR CCD detector. The template file XDS-MARCCD.INP handles those. The pixel size, etc. are taken automatically from the frame headers. This detector type is also s

Re: [ccp4bb] XDS INP

Dear Fred, Actually I'm not very sure the detector type is MX300. The site file of HKL2000 is in the folder called MX300. I guess the detector is MX300 because there are another folder call PILATUS6M. In the def.site, I can see {dectec} {CCD unsupported-m300}. And there seems no m300 dec

[ccp4bb] Fwd: [ccp4bb] XDS INP

Dear Lu you can freely download the tutorial from here: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_Page You can check if your detector is supported here: http://xds.mpimf-heidelberg.mpg.de/html_doc/detectors.htm Best Fulvio > Il giorno 07/mag/2015, alle ore 10:33, luzu

Re: [ccp4bb] XDS INP

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Lu zuokun, the web site http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/detectors.html lists all the detectors supported by XDS. There are some graphical user interfaces for XDS which are very good not only for beginners. One I can r

[ccp4bb] XDS INP

Dear all, I'm a XDS beginner and the first problem I encounter was the INP file. The detector type is MX300. Is the detector supported by XDS? How to modified the INP file? The sitefile of HKL2000 was attached. Can anyone provide some tutorial to use XDS? Best wishes! Lu zuokun

Re: [ccp4bb] XDS Processing with Translated Detector and Radiation Sensitive Crystals

Hi Christopher, you should also limit the resolution to say 6 A on the first pass to get your correct cell parameters. Your low I/sigI suggests that the indexing did not pick up the correct orientation of the crystal. You should also see this in your INTEGRATE.LP file if you look at the spot pr

Re: [ccp4bb] XDS Processing with Translated Detector and Radiation Sensitive Crystals

Hope this is of use. Good luck Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Christopher Barnes Sent: Thursday, April 16, 2015 4:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] XDS Processing with Translated Detector and Radiation Sen

[ccp4bb] XDS Processing with Translated Detector and Radiation Sensitive Crystals

Hi all, I am having trouble processing synchrotron data with XDS for a large unit cell protein complex (Spacegroup P2, Cell 225 x 256 x 430). My crystals diffract to 3.1 Angstrom, but at this resolution we had significant spatial overlaps. To alleviate this we translated the detector 40 mm in b

Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

Yes, unfortunately an "orientation matrix" is completely useless without a frame of reference. All it does is tell you where the cell axes lie relative to "X", "Y" and "Z", but "X" may be the x-ray beam, or sometimes that is "Z" and "X" is the spindle axis. Different people have different and

Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

On Sun, 28 Dec 2014 15:37:22 -0600, Igor Petrik wrote: ... > DIRECT BEAM COORDINATES (REC. ANGSTROEM) 0.003134 0.005401 1.020962 > DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM1230.87 1260.93 > DETECTOR ORIGIN (PIXELS) AT 1226.25 1252.96 > CRYSTAL TO DETECTOR DISTAN

Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

Takanori and Pierre, Thank you for your quick responses. If you read my post you will see that I used the xds2mos.py script to convert the xds orientation to Mosflm format, but this gives me a result that is inconsistent with the matrix calculated directly by moslfm or DENZO. For orthorombic space

Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

Hi, xdsme has xds2mos.py script. https://code.google.com/p/xdsme/ https://code.google.com/p/xdsme/source/browse/XOconv/xds2mos.py Best regards, Takanori Nakane On 2014/12/29 6:37, Igor Petrik wrote: I am working on a small project which requires me to obtain the proper orientation of a cryst

Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

(I think) these matrices are roughly 180 degrees apart, so they may just correspond to different signs of the axes Phil On 28 Dec 2014, at 21:37, Igor Petrik wrote: > I am working on a small project which requires me to obtain the proper > orientation of a crystal lattice with respect to the g

[ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

I am working on a small project which requires me to obtain the proper orientation of a crystal lattice with respect to the gonistat and source. I have until now successfully used the matrices from Mosflm and DENZO, which are consistent with each other and define the orientation of the reciprocal l

[ccp4bb] XDS and XDSGUI latest versions

Hi everybody, pls note that the XDS version that you might have installed a year ago will expire on Dec 31, and there's a new version at http://xds.mpimf-heidelberg.mpg.de/ . The changes are: support for Eiger, support for XZ compressed files, and assorted small fixes. The XDS documentation is st

Re: [ccp4bb] XDS

Thank you all for the suggestions. What worked better for me was to run XDS with different batches of images and to merge them later with XSCALE. Best, Almudena 2014-09-29 11:56 GMT+02:00 Almudena Ponce Salvatierra : > Dear all, > > I would like to ask something regarding XDS. Is it possible,

Re: [ccp4bb] XDS

, September 29, 2014 12:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] XDS Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like defining twice the data range

[ccp4bb] AW: [ccp4bb] XDS

Auftrag von Almudena Ponce Salvatierra Gesendet: Montag, 29. September 2014 11:57 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] XDS Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like

Re: [ccp4bb] XDS

Hi,  Another option to do it in xds (following advice of a Kay) is to rename the frames you don't like differently than the template.  Boaz Original message From: Almudena Ponce Salvatierra Date: To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb

Re: [ccp4bb] XDS

Hi Almudena, Greeting from Oulu.Other possibility would be, process the group of Frames separately in XDS and merge them in the end. Thank you Rajesh On Mon, Sep 29, 2014 at 12:56 PM, Almudena Ponce Salvatierra < maps.fa...@gmail.com> wrote: > Dear all, > > I would like to ask something

Re: [ccp4bb] XDS

Hi Almudena, if you run XDS through xia2, you can define multiple wedges in your info: BEGIN SWEEP SWEEP1 IMAGE image_0001.cbf DIRECTORY /path/to/files/ START_END 1 900 END SWEEP BEGIN SWEEP SWEEP2 IMAGE image_0001.cbf DIRECTORY /path/to/files/ START_END 1001 1200 END SWEEP Andreas On 29/

[ccp4bb] XDS

Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like defining twice the data range DATA_RANGE= 1 900 !DATA_RANGE= 901 1000 DATA_RANGE= 1001 1200 Is there a way to do so? to leave ou

Re: [ccp4bb] XDS, refinement not converge

Hi, Kay, it happened during INTEGRATE step. I used REFINE(INTEGRATE)=BEAM ORIENTATION AXIS CELL ! DISTANTCE and all the warning is gone. I will also try your suggestion to see if it gives any difference. REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION ! AXIS CELL Thanks! Charles On Mon, Sep 22,

Re: [ccp4bb] XDS, refinement not converge

Charles, your posting does not provide enough detail to base advice on. First of all, it's a warning and probably there is no reason to worry - but one has to look at the .LP files to be sure. Second, it is not clear whether the warning is printed by IDXREF or by INTEGRATE. If it's IDXREF

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