[ccp4bb] XSCALE bugfix
Dear academic XDS/XSCALE users, there's a bug in XSCALE, in the BUILT=20190606 of the XDS program package. The bug was not in present in earlier versions. It is corrected in the latest BUILT=20190806 which is available from the download section of http://xds.mpimf-heidelberg.mpg.de . The release notes in the documentation that can be downloaded as a tar-file from that site is updated. The release notes at http://xds.mpimf-heidelberg.mpg.de/html_doc/Release_Notes.html will soon be updated. Those XSCALE users who downloaded BUILT=20190606 should upgrade, and consider re-xscaling. best wishes, Kay To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] XSCALE!!! ERROR
Hello Bashir, Maybe it's because your dataset present too much weak diffraction spots. You can try to change the setting for the strong pixel detection. You can Try to decrease a little bit de I/sigma. Have you define the resolution range? I read on your message that you resolution start at 5 A. To my mind it's too high, you should have more low resolution. Perhaps your problem com from this specificity of you dataset. Try first to set your resolution range from inf. to 3.25 Hope to help you. Nicolas Le 07/09/11 21:39, Muhammed bashir Khan a écrit : Dear All; I am trying to to xsale several data sets together, but it gives an error of !!! ERROR !!! INSUFFICIENT NUMBER OF COMMON STRONG REFLECTIONS. PROGRAM IS UNABLE TO PRODUCE A SCALED DATA SET. resolution of data sets is ranged from 3.25 to 5A Any suggestion will be highly encouraged. Thanks in adv. Bashir
Re: [ccp4bb] XSCALE!!! ERROR
Am Mittwoch 07 September 2011 21:39:07 schrieb Muhammed bashir Khan: Dear All; I am trying to to xsale several data sets together, but it gives an error of !!! ERROR !!! INSUFFICIENT NUMBER OF COMMON STRONG REFLECTIONS. PROGRAM IS UNABLE TO PRODUCE A SCALED DATA SET. resolution of data sets is ranged from 3.25 to 5A Any suggestion will be highly encouraged. Thanks in adv. Bashir Hi Bashir, we had already such an error twice. In one case one of the integration failed and the XDS_ASCII.HKL was rubbish. there was the wrong space group and so no common reflections. In an other case many overloaded reflection led to too few reflections which could be scaled together, because more than 50 % of the reflections were rejected in the CORRECT step. In this case we had to recollect the data. Christian
Re: [ccp4bb] XSCALE!!! ERROR
Original Message Subject: XSCALE!!! ERROR Date: Wed, 7 Sep 2011 21:39:07 +0200 From: Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at Dear All; I am trying to to xsale several data sets together, but it gives an error of !!! ERROR !!! INSUFFICIENT NUMBER OF COMMON STRONG REFLECTIONS. PROGRAM IS UNABLE TO PRODUCE A SCALED DATA SET. resolution of data sets is ranged from 3.25 to 5A Any suggestion will be highly encouraged. Thanks in adv. Bashir Bashir, the problem is what the error message tries to convey: scaling _requires_ common reflections, and there are two or more partitions of your several data sets which do not overlap in this sense. xscale prints out the number of common reflections ... inspect the list in XSCALE.LP ! Two ways to proceed: - find out whether there are datasets that have no common reflections with any of the others. Remove those, and scale the others. - add more datasets HTH, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature smime.p7s. smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] XSCALE!!! ERROR
Dear All; I am trying to to xsale several data sets together, but it gives an error of !!! ERROR !!! INSUFFICIENT NUMBER OF COMMON STRONG REFLECTIONS. PROGRAM IS UNABLE TO PRODUCE A SCALED DATA SET. resolution of data sets is ranged from 3.25 to 5A Any suggestion will be highly encouraged. Thanks in adv. Bashir -- Muhammad Bashir Khan ** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522
[ccp4bb] XSCALE vs scala
Hello all, I've been converting my XDS files (XDS_ASCII.hkl) to mtz using pointless and then running scala to get the work mtz. I like this procedure because I get useful info, (such as Rpim), that I don't know how to get otherwise. I there any advantage/disadvantage of using this procedure instead of scaling and converting with XSCALE and XDSCONV? Thanks! Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal It's very hard to make predictions... especially about the future - Niels Bohr
[ccp4bb] Fwd: [ccp4bb] XSCALE vs scala
Begin forwarded message: From: Graeme Winter graeme.win...@googlemail.com Date: March 4, 2011 4/3/11 - 4:51 To: José Trincão trin...@dq.fct.unl.pt Subject: Re: [ccp4bb] XSCALE vs scala Hi Jose, if you are following the usual XDS procedure, the data will have already been scaled by the XDS CORRECT step. XSCALE will perform essentially the same scaling, but for more than one sweep. I usually use scala to merge data from XDS and XSCALE, using scales constant - however you could also use XDSSTAT. Best wishes, Graeme On 4 March 2011 16:26, José Trincão trin...@dq.fct.unl.pt wrote: Hello all, I've been converting my XDS files (XDS_ASCII.hkl) to mtz using pointless and then running scala to get the work mtz. I like this procedure because I get useful info, (such as Rpim), that I don't know how to get otherwise. I there any advantage/disadvantage of using this procedure instead of scaling and converting with XSCALE and XDSCONV? Thanks! Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal It's very hard to make predictions... especially about the future - Niels Bohr José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal It's very hard to make predictions... especially about the future - Niels Bohr
[ccp4bb] XSCALE
Hello All; I've just started using XDS and have scaled three data sets from the same crystal - unmerged. It was a SAD experiment My question is concerning which R values to use as data processing statistics. I don't find any Rsymm or even Redundancy values in the LP files. I came across an exmple where Rr.i.m / Rmeas was reported but I don't understand the distinction between these values. Thank you in advance. Anna
Re: [ccp4bb] XSCALE
Dear Anna, Something I find useful is to convert the output of XSCALE (unmerged) to MTZ format using pointless (pointless -c xdsin SCALED.XDS hklout sorted.mtz) then to merge the reflections with Scala: scala hklin sorted.mtz hklout scaled.mtz eof run 1 all scales constant anomalous on # or off eof This will write out the merging statistics in the usual scala way - very helpful. You also get all the loggraphs etc. Best wishes, Graeme On 5 August 2010 15:07, anna delprato del_...@yahoo.com wrote: Hello All; I've just started using XDS and have scaled three data sets from the same crystal - unmerged. It was a SAD experiment My question is concerning which R values to use as data processing statistics. I don't find any Rsymm or even Redundancy values in the LP files. I came across an exmple where Rr.i.m / Rmeas was reported but I don't understand the distinction between these values. Thank you in advance. Anna
Re: [ccp4bb] XSCALE
anna delprato wrote: Hello All; I've just started using XDS and have scaled three data sets from the same crystal - unmerged. It was a SAD experiment My question is concerning which R values to use as data processing statistics. I don't find any Rsymm or even Redundancy values in the LP files. I came across an exmple where Rr.i.m / Rmeas was reported but I don't understand the distinction between these values. Thank you in advance. Anna Dear Anna, The classical R-sym (on intensities) in the files XCALE.LP and CORRECT.LP is called R-FACTOR observed. There is another R-sym value called R-meas, plus something called Rmrgd-F defined in Diederichs Karplus (1997), Nature Struct. Biol. 4, 269-275 (this is all given above the tables in the .LP files). In case of anomalous diffraction, there is no R-ano as such but other values are provided. WRT the redundancy, I am afraid you have to recompute an approximate value yourself using the number of observations and number of unique reflections (this is what I do all the time). I suppose one could always write a jiffy program to compute the correct values using both files INTEGRATE.HKL and XDS_ASCII.HKL, but I haven't done it myself... Yet ? Fred.
[ccp4bb] Fwd: [ccp4bb] XSCALE
WRT the redundancy, I am afraid you have to recompute an approximate value yourself using the number of observations and number of unique reflections (this is what I do all the time). I suppose one could always write a jiffy program to compute the correct values using both files INTEGRATE.HKL and XDS_ASCII.HKL, but I haven't done it myself... Yet ? No need to do that - you can use the xdspub command within XDSi: http://cc.oulu.fi/~pkursula/xdsi.html http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSi which gives this kind of output: Final data processing statistics SPACE_GROUP_NUMBER= 197 UNIT_CELL_CONSTANTS=78.0978.0978.09 90.000 90.000 90.000 INPUT_FILE= ./XDS_ASCII.HKL XDS_ASCII Unique reflections 11084. High res. shell 1.65-1.50 Redundancy 4.3( 1.9) R(sym) 3.1( 53.1) R(meas) 3.5( 70.7) R(mergd-F) 7.8(106.0) I/s(I) 25.1( 1.5) completeness 86.2( 57.3) Best, Luca Luca Jovine, Ph.D. Group Leader EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.se W3: http://jovinelab.org
[ccp4bb] Fwd: [ccp4bb] XSCALE (II)
Apologies for the repetition, but only the first link: http://cc.oulu.fi/~pkursula/xdsi.html is for the xdspub program that produces the output I attached. The other one has the same name, but does something else! Luca
Re: [ccp4bb] Fwd: [ccp4bb] XSCALE
Another very nice script to run and collect statistics from XDS is xdsme from Pierre Legrand http://code.google.com/p/xdsme/ Daniel Le 05/08/2010 16:55, Jovine Luca a écrit : WRT the redundancy, I am afraid you have to recompute an approximate value yourself using the number of observations and number of unique reflections (this is what I do all the time). I suppose one could always write a jiffy program to compute the correct values using both files INTEGRATE.HKL and XDS_ASCII.HKL, but I haven't done it myself... Yet ? No need to do that - you can use the xdspub command within XDSi: http://cc.oulu.fi/~pkursula/xdsi.html http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSi which gives this kind of output: Final data processing statistics SPACE_GROUP_NUMBER= 197 UNIT_CELL_CONSTANTS=78.0978.0978.09 90.000 90.000 90.000 INPUT_FILE= ./XDS_ASCII.HKL XDS_ASCII Unique reflections 11084. High res. shell 1.65-1.50 Redundancy 4.3( 1.9) R(sym) 3.1( 53.1) R(meas) 3.5( 70.7) R(mergd-F) 7.8(106.0) I/s(I) 25.1( 1.5) completeness 86.2( 57.3) Best, Luca Luca Jovine, Ph.D. Group Leader EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.se W3: http://jovinelab.org
