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Hi Tim, this is incorrect. XSCALE determines the relative scale and B in a first step (this is what you describe). It then, in a second step, re-determines all scale factors (exactly as CORRECT does for the individual data sets), at the exact same supporting points that CORRECT used. (This avoids over-fitting which would result from a scaling model with different basis functions; a worry that I have when people use SCALA/AIMLESS after CORRECT without taking precautions.) The resulting scale factors are written to files MODPIX*.cbf, DECAY*.cbf, ABSORP*.cbf for inspection. Thirdly, it produces statistics and writes output files. best, Kay On Wed, 12 Nov 2014 11:22:51 +0100, Tim Gruene <[log in to unmask]> wrote: >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > >Dear Wolfram Tempel, > >there might be some confusion about terms. > >It is correct that xscale scales several data sets together. However, >in crystallography, 'merging' might be the better term for this process. > >Crystallographic 'Scaling' is far more complicated than 'merging'. It >applies correction factors which try to make up for experimental >errors in your data set. These corrections include the sigma-values, >which is particularly important for experimental phasing. In that >respect it can actually hamper the data quality if you >(crystallographically) scale your data twice, although the effect is >rather subtle. > >CORRECT carries out these corrections, hence CORRECT scales your data >set, while XSCALE does not repeat this step - it "only" merges your >data in the sense that it puts your data on a common scale. This is >the application of a not too difficult mathematical formula (which is >listed in the xds wiki, but I don't remember the URL). > >Regards, >Tim > >On 11/11/2014 10:07 PM, Sudhir Babu Pothineni wrote: >> >> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale >> >> XSCALE >> <http://www.mpimf-heidelberg.mpg.de/%7Ekabsch/xds/html_doc/xscale_parameters.html> >> >> >is the scaling program of the XDS suite. It scales reflection files >> (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT >> step of XDS already scales an individual dataset, XSCALE is only >> /needed/ if several datasets should be scaled relative to another. >> However, it does not deterioriate a dataset if it is "scaled again" >> in XSCALE, since the supporting points of the scalefactors are at >> the same positions in detector and batch space. The advantage of >> using XSCALE for a single dataset is that the user can specify the >> limits of the resolution shells. >> >> _Scaling with scala/aimless_ >> >> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Scaling_with_SCALA_%28or_better:_aimless%29 >> >> >> >> -Sudhir >> >> >> *************************** Sudhir Babu Pothineni GM/CA @ APS 436D >> Argonne National Laboratory 9700 S Cass Ave Argonne IL 60439 >> >> Ph : 630 252 0672 >> >> >> >> >> On 11/11/14 14:42, wtempel wrote: >>> Thank you Boaz. So if CORRECT can do a fully corrected scaling, >>> are there no corrections that XSCALE might apply to XDS_ASCII.HKL >>> data that are beyond CORRECT's capabilities? Wolfram >>> >>> >>> On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan >>> <[log in to unmask] <mailto:[log in to unmask]>> wrote: >>> >>> Hi, >>> >>> I actually choose the option 'constant' further down in the >>> aimless gui but I guess the effect is similar to 'onlymege'. >>> >>> Boaz >>> >>> /Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University >>> of the Negev Beer-Sheva 84105 Israel >>> >>> E-mail: [log in to unmask] <mailto:[log in to unmask]> Phone: >>> 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or >>> 972-8-646-1710 / // // / >>> >>> / >>> >>> ------------------------------------------------------------------------ >>> >>> >*From:* CCP4 bulletin board [[log in to unmask] >>> <mailto:[log in to unmask]>] on behalf of wtempel >>> [[log in to unmask] <mailto:[log in to unmask]>] *Sent:* Tuesday, >>> November 11, 2014 9:50 PM *To:* [log in to unmask] >>> <mailto:[log in to unmask]> *Subject:* [ccp4bb] To scale or >>> not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS >>> >>> Hello all, in a discussion >>> >>> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307&L=CCP4BB&H=1&P=186901> >>> >>> >>> >on this board, Kay Diederichs questioned the effect of scaling >>> data in AIMLESS after prior scaling in XDS (CORRECT). I >>> understand that the available alternatives in this work flow are >>> to specify the AIMLESS ‘onlymerge’ command, or not. Are there any >>> arguments for the preference of one alternative over the other? >>> Thank you for your insights, Wolfram Tempel >>> >>> >>> >>> >> >> > >- -- >- -- >Dr Tim Gruene >Institut fuer anorganische Chemie >Tammannstr. 4 >D-37077 Goettingen > >GPG Key ID = A46BEE1A > >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.4.12 (GNU/Linux) > >iD8DBQFUYzT7UxlJ7aRr7hoRAuO2AJ9P3kJAjP+8wWjXRvkZwgDs9UOo3ACfb1En >67VgyyqCTX6j5vOz3xMVwqE= >=ooTC >-----END PGP SIGNATURE-----