Dear Herman, some pros and cons are documented at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Wishlist#Would_be_nice_to_have , and the workaround is at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings . These XDSwiki articles are old, and nobody has contributed to the discussion since 2007 (after all, is is a Wiki!), so there has not been much reason for a change. Tim is right in that usage of INCLUDE_RESOLUTION_RANGE does not fit well at the COLSPOT stage, since COLSPOT "knows" nothing about wavelength, distance, pixel size and so on. If there is agreement among XDS users that IDXREF should take INCLUDE_RESOLUTION_RANGE into account, there is a good chance that the next version of XDS will do that.
best, Kay On Wed, 20 Mar 2013 09:29:47 +0000, 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 > >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > >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/ > >iD8DBQFRSOFJUxlJ7aRr7hoRAo6TAKC+BePgeODbDyngO7N8vCE4CnjxmQCfS5cP >srShHNz1sDK0EMHSbE3fDwA= >=kAwf >-----END PGP SIGNATURE-----
