On Thu, 21 Mar 2013 08:28:27 +0000, herman.schreu...@sanofi.com wrote: >Dear Tim, > >It could be that COLSPOT does not rely on experimental setup parameters. >However, XDS must have reasonably close starting values for distance, direct >beam position etc., otherwise the autoindexing would fail, so the information >to calculate an approximate TRUSTED_REGION is available.
TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE are orthogonal concepts; both are input by the user and not calculated by the program. > >For good data, a limited spot range usually works as well. However, for the >weakly diffracting bad crystals with ice rings, salt spots, multiple >diffraction patterns etc., one often needs the full range and often needs >several tries with different parameters before indexing is successful. Since >it is only cpu-time, it is the least of my worries and, as you mention, it is >not bad to be forced to think once in a while instead of just clicking buttons >in GUI's. Nevertheless I plan to release a GUI for xds soon; among other things, this enables to visualize and change TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE . best, Kay > >Best regards, >Herman > > > >-----Original Message----- >From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] >Sent: Wednesday, March 20, 2013 11:17 PM >To: Schreuder, Herman R&D/DE >Cc: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Resolution limit of index in XDS > >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > >Dear Herman, > >the short answer might be that at the stage of COLSPOT the term 'resolution' >has a limited meaning because COLSPOT does not rely on the experimental setup >like distance and beam direction, so the term 'resolution limit' is >conceptually not applicable at this stage. > >Indexing does often not require the full data set, you can reduce the >"SPOT_RANGE" if you are worried about processing time, or by a multi-CPU >machine. > >One of the great advantages of XDS is that it asks you to think at a level >higher than the average MS-Windows user while processing your data, so the >effort to figure out the three numbers to set the TRUSTED_REGION is in line >with the philosphy of XDS as I understand it. > >But you are right, I do not have access to the source of XDS and I am not the >person to address a request to. > >Kind regards, >Tim > >On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote: >> Dear Tim, but probably I should adres this to Kai Diederichs, >> >> not including the resolution cutoff in COLSPOT and IDXREF is a feature >> of XDS I do not understand at all. For most cases, it may not matter >> since only the strong spots are used, but what are the advantages? >> >> In fact there are disadvantages, especially when dealing with poorly >> diffracting difficult data sets: -when a crystallographer imposes a >> resolution limit, there are usually good reasons for it. >> -outside the resolution limit, there may be ice rings or contaminating >> salt spots, which make the autoindexing fail. -when processing 900 >> frame Pilatus data sets, running COLSPOT on the complete detector >> surface takes significantly longer then running it only on the center >> region. >> >> Of course, one could fudge a resolution cutoff by translating >> resolution into pixels and then calculating a TRUSTED_REGION, or >> manually editing the SPOT.XDS file, but this is a lot of extra and in >> my view unneccessary work. >> >> I would really consider using the resolution cutoff for COLSPOT as >> well. >> >> Best, Herman >> >> >> -----Original Message----- From: CCP4 bulletin board >> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: >> Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: >> Re: [ccp4bb] Resolution limit of index in XDS >> >> Dear Niu, >> >> indexing relies on strong reflections only, that is (in very >> brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the >> relections collected in COLSPOT which in turn are used by IDXREF. >> You can work around this, however, by making use of TRUSTED_REGION and >> set it to e.g. 0.7 or 0.6 (you can use adxv to translate resolution >> into pixel and then calculate the fraction you need to set the second >> number in TRUSTED_REGION to (or the first if you want to exclude the >> inner resolution reflections - I remember one data set where this was >> essential for indexing - DNA was involved >> there) >> >> Best, Tim >> >> On 03/19/2013 08:53 PM, Niu Tou wrote: >>> Dear All, >> >>> Is there any command can set the resolution limit for index step in >>> XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to >>> be a definition of resolution range after index step as it says: >> >>> INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by >>> DEFPIX,INTEGRATE,CORRECT >> >>> Thanks! Niu >> >> >> > >- -- >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) >Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > >iD8DBQFRSjVtUxlJ7aRr7hoRApZhAJ9RFBs8D9NGjgLY3KOoNHhNtdOWggCgj7U0 >zY7jEFDYZfl0Umb9E1Bzs1U= >=+HjR >-----END PGP SIGNATURE-----
