Re: [ccp4bb] xds and cell refinement in cP
Hi Jan, there is now a new version of XDS at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ The old versions of XDS had a very low radius of convergence for the cell refinement in high-symmetry spacegroups. This is fixed in the latest version, and it has other enhancements, too. best, Kay Jan Abendroth schrieb: Hi all, I am running into a strange behaviour fo xds for a primitive cubic data set. Neither in the INTEGRATE nor in the CORRECT step the cell parameters are refined and stay exactly at the value specified in XDS.INP. R-factors and I/sigmas of the XSCALE run look suspiciously high/low. When I reduce the symmetry to tetragonal and run an otherwise identical XDS.INP script, the cell parameters are refined again. Any ideas? Thanks a bunch Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature smime.p7s. smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] xds and cell refinement in cP
Jan Abendroth schrieb: Hi all, I am running into a strange behaviour fo xds for a primitive cubic data set. Neither in the INTEGRATE nor in the CORRECT step the cell parameters are refined and stay exactly at the value specified in XDS.INP. R-factors and I/sigmas of the XSCALE run look suspiciously high/low. When I reduce the symmetry to tetragonal and run an otherwise identical XDS.INP script, the cell parameters are refined again. Any ideas? Thanks a bunch Jan Jan, I think that in the cubic system you cannot refine cell and distance at the same time. If you have, in XDS.INP, REFINE(INTEGRATE)=DISTANCE CELL and similar for REFINE(CORRECT) then XDS will keep the cell at the input value, and refine the distance. So just remove DISTANCE from both lines in XDS.INP to have it refine the cell instead. The fact that the R-factors and I/sigmas of the XSCALE run look suspiciously high/low is unrelated, I'd say. HTH, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature smime.p7s. smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] xds and cell refinement in cP
Hi Jan, Always worth a try is to process the data in P1 then assigning the symmetry in CORRECT - that way the cell constants can refine to what they want to. It also means you can check that the symmetry actually is cubic. For the majority of data sets in my experience it makes little difference whether you assign the lattice constraints during integration, unless they're wrong. Cheers, Graeme 2009/10/8 Jan Abendroth jan.abendr...@gmail.com: Hi all, I am running into a strange behaviour fo xds for a primitive cubic data set. Neither in the INTEGRATE nor in the CORRECT step the cell parameters are refined and stay exactly at the value specified in XDS.INP. R-factors and I/sigmas of the XSCALE run look suspiciously high/low. When I reduce the symmetry to tetragonal and run an otherwise identical XDS.INP script, the cell parameters are refined again. Any ideas? Thanks a bunch Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
