Re: [ccp4bb] discontinuous data wedges in XDS
Hi Bert, xia2 is your friend in cases like this. This program is a real boon for the lazy crystallographer. All you need to type is: xia2 -3d /path/to/images and xia2 will automagically index, integrate and scale all of the sweeps together. Add the "-atom Se" flag (atom name as appropriate) to be sure you keep anomalous signal in the final mtz file. See http://www.ccp4.ac.uk/xia/ for more info. Cheers, Stephen On 4/29/08, Van Den Berg, Bert <[EMAIL PROTECTED]> wrote: > > > > Hi all, > > is it possible to input discontinuous data wedges into XDS (obtained from > for example inverse beam sweeps)? (So wedge se1 goes from 0-90 deg (image > 1-90), se2 from 180-270 (image 1-90), etc). Or do I have to rename > everything so that I get one data file in which the rotation ranges are > continuous? > > Thanks, Bert > > Bert van den Berg > University of Massachusetts Medical School > Program in Molecular Medicine > Biotech II, 373 Plantation Street, Suite 115 > Worcester MA 01605 > Phone: 508 856 1201 (office); 508 856 1211 (lab) > e-mail: [EMAIL PROTECTED] > http://www.umassmed.edu/pmm/faculty/vandenberg.cfm > > -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
Re: [ccp4bb] discontinuous data wedges in XDS
Klaus Futterer schrieb: Is it not sufficient to first integrate the one wedge, then use this wedge as a reference data set when integrating the second one? (REFERENCE_DATA_SET= ../wedge01/XDS_ASCII.HKL) Klaus no, the REFERENCE_DATA_SET (first wedge of data) would then not be merged with the second wedge (which is the data integrated in that XDS run). Specifying a REFERENCE_DATA_SET would give you R-factors of the two wedges w.r.t. each other, and would also influence the scaling (which would not be intended in this case). Merging should be done with XSCALE (as Jürgen wrote already). best, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] discontinuous data wedges in XDS
Is it not sufficient to first integrate the one wedge, then use this wedge as a reference data set when integrating the second one? (REFERENCE_DATA_SET= ../wedge01/XDS_ASCII.HKL) Klaus - Klaus Fütterer, Ph.D. School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: [EMAIL PROTECTED] Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/ - On 29 Apr 2008, at 22:57, Juergen Bosch wrote: You can integrate them as separate wedges (in different directories), then later merge them (XDS_ASCII.HKL) in Xscale. Make sure though you have the orientation right and starting angles etc. You'll have to first refine one wedge, then once you are happy with it copy the GXPARM.XDS into the other directories (as XPARM.XDS) and input those parameters into XDS..INP Juergen Van Den Berg, Bert wrote: Hi all, is it possible to input discontinuous data wedges into XDS (obtained from for example inverse beam sweeps)? (So wedge se1 goes from 0-90 deg (image 1-90), se2 from 180-270 (image 1-90), etc). Or do I have to rename everything so that I get one data file in which the rotation ranges are continuous? Thanks, Bert Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Biotech II, 373 Plantation Street, Suite 115 Worcester MA 01605 Phone: 508 856 1201 (office); 508 856 1211 (lab) e-mail: [EMAIL PROTECTED] http://www.umassmed.edu/pmm/faculty/vandenberg.cfm -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Re: [ccp4bb] discontinuous data wedges in XDS
You can integrate them as separate wedges (in different directories), then later merge them (XDS_ASCII.HKL) in Xscale. Make sure though you have the orientation right and starting angles etc. You'll have to first refine one wedge, then once you are happy with it copy the GXPARM.XDS into the other directories (as XPARM.XDS) and input those parameters into XDS..INP Juergen Van Den Berg, Bert wrote: Hi all, is it possible to input discontinuous data wedges into XDS (obtained from for example inverse beam sweeps)? (So wedge se1 goes from 0-90 deg (image 1-90), se2 from 180-270 (image 1-90), etc). Or do I have to rename everything so that I get one data file in which the rotation ranges are continuous? Thanks, Bert Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Biotech II, 373 Plantation Street, Suite 115 Worcester MA 01605 Phone: 508 856 1201 (office); 508 856 1211 (lab) e-mail: [EMAIL PROTECTED] http://www.umassmed.edu/pmm/faculty/vandenberg.cfm -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
[ccp4bb] discontinuous data wedges in XDS
Hi all, is it possible to input discontinuous data wedges into XDS (obtained from for example inverse beam sweeps)? (So wedge se1 goes from 0-90 deg (image 1-90), se2 from 180-270 (image 1-90), etc). Or do I have to rename everything so that I get one data file in which the rotation ranges are continuous? Thanks, Bert Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Biotech II, 373 Plantation Street, Suite 115 Worcester MA 01605 Phone: 508 856 1201 (office); 508 856 1211 (lab) e-mail: [EMAIL PROTECTED] http://www.umassmed.edu/pmm/faculty/vandenberg.cfm
