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

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:

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 <ww2...@columbia.edu> Date: 21/11/2016 19:05 (GMT+02:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] XDS que

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

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

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

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

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,

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