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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 [mailto:[log in to unmask]] 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 loose a lot of information. I would like to offer a different opinion to Graeme's: You can read XDS_ASCII.HKL into pointless and aimless and provide aimless with the option 'onlymerge'. This way aimless merges the data, but it does not rescale them. XDS performs a couple of corrections in the CORRECT step, the output of which is XDS_ASCII.HKL. And while XDS is extremely well documented, I am not sure aimless takes into account how XDS treats the data. I would therefore trust the step of scaling to the same author and continue with XDS_ASCII.HKL. Best, Tim On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote: > 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 and > another using INTEGRATE.HKL and I found that in the run using > XDS_ASCII.HKL little lesser total number of observation but marginally better statistics. > > Thanks > Nishant > > On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster > <[log in to unmask]> > > wrote: > > 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, Wei Wang <[log in to unmask]> wrote: > >> 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 follow the XDS-Aimless route, then probably I > >> should let Aimless do "skip scaling and only merge"? Please > >> elucidate me on this issue. > >> > >> Regards, > >> > >> Wei > > -- > Dr. Nishant Kumar Varshney, > IISc-ICTP Fellow > XRD2 Beamline, Elettra-Sincrotrone, > In Area Science Park, > Basovizza, S.S. 14, Km 163,5, > 34012 Trieste, Italy > +39-040-375 8737 (office ESP4 P1 031) > +39-040-375-8435 (XRD2 beamline) > +39 3318809798 (Mobile) -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/102 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom