I was a little provokative. A GUI with a viewer would actually be an excellent idea since it allows one to see what one is doing, which would be of great help for difficult data sets. Nevertheless, since XDS is part of many automated pipelines, the possibility to run XDS offline with a command file should not be touched. If IDXREF would take the INCLUDE_RESOLUTION_RANGE into account, I am sure this would improve the performance of XDS.
Best regards and thank you for the work you put into XDS! Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Thursday, March 21, 2013 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution limit of index in XDS 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-----
