Hello Kay, you said the o-word, and you are familiar with the inner workings of XDS. Has the data-to-parameter ratio in even complex scaling models become so small that a doubling (worst case) of model parameters would be a serious concern? Could one detect such overfitting by, say, comparing (molecular) model R-factors between refinement against the once (CORRECT) scaled or twice (CORRECT+AIMLESS) scaled data? Thank you, Wolfram
On Wed, Nov 12, 2014 at 10:32 AM, Kay Diederichs < [email protected]> wrote: > 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 <[email protected]> > 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 > >>> <[email protected] <mailto:[email protected]>> 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: [email protected] <mailto:[email protected]> Phone: > >>> 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or > >>> 972-8-646-1710 / // // / > >>> > >>> / > >>> > >>> > ------------------------------------------------------------------------ > >>> > >>> > >*From:* CCP4 bulletin board [[email protected] > >>> <mailto:[email protected]>] on behalf of wtempel > >>> [[email protected] <mailto:[email protected]>] *Sent:* Tuesday, > >>> November 11, 2014 9:50 PM *To:* [email protected] > >>> <mailto:[email protected]> *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----- >
