Hmm... Thinking about this it may not be too hard to do with XDS. May involve a certain amount of fiddling though.
If you do the first stages of XDS processing, namely XYCORR, INIT, COLSPOT & IDXREF you will end up with a spot file (SPOT.XDS) from colspot and with indices attached from IDXREF. Once you have processed the strongest lattice, you could remove the spots indexed for that "run" from the SPOT.XDS file from COLSPOT and rerun IDXREF - this should the index the remaining reflections and give you an XPARM file you can use for integration. As Clemens says, the measurements may be suboptimal, but it is certainly worth a go and should not really be that hard. I suspect a certain amount of plaing with sed and grep here will be necessary. XDS *will* complain a lot though saying that it can index < 70 % of reflections. This is to be expected. You can give XDS the unit cell and symmetry if known and it will use these for clustering the difference vectors generated from the spot positions. In your case this is a good idea, as there will be a lot of noise (which difference vector indexing is quite sensitive to) from the spots from the other lattices. What I would definitely do is run once with the strongest lattice, then copy the files to another directory for the processing of the second strongest lattice and so on. Good luck, Graeme -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Clemens Vonrhein Sent: 18 February 2008 13:35 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] indexing multiple lattices On Mon, Feb 18, 2008 at 01:58:59PM +0100, Jason Greenwald wrote: > I have a crystal that grows with multiple lattices despite the fact > that the crystals look more or less like single crystals under the > microscope. > > With a lot of guesswork I am able to index with mosflm by carefully > selecting spots that appear to be in the same lattice. > Now I would like to use the known cell and symmetry to index more > datasets that have the same "twinning" problem. This is real fun to do - you can even index/integrate these several lattices: gives you higher multiplicity etc. But (there's always a but): be careful in using the data. It is very likely that a very large proportion of reflexions overlap - either completely or partially. There are ways of classifying these reflections, but a better way is to use a program that can process these twinned crystals (and no: neither XDS nor MOSFLM can ... at least not without hacking the source code or doing some other weird stuff). > Is there any way to do a search of crystal orientation matrices with > a known cell to find the best fit to the diffraction pattern? > The data were collected on the Pilatus6M detector so I am limited to > mosflm and XDS for processing. Both packages always trying to index > the crystal without using the known cell and symmetry to get the > orientation matrix. Not quite true: in both packages you can give the cell and symmetry. I'm not sure how it is handled internally exactly by those programs - but it seems to me that MOSFLM will use this information only after autoindexing to pick a solution closests to the user-given cell/symmetry. I _think_ XDS might use that info a bit earlier during indexing. But I could be wrong on both accounts. > I thought of writing a script to do a full search (testing all > orientations sequentially) in mosflm but I thought that I should > submit to the experts before I try anything. If you want some more detailed 'recipe' for processing non-merohedrally twinned crystals with XDS, please let me know directly. However, if you're planning to use that data for experimental phasing on a medium to small signal: don't get your hopes up. It might be enough for molecular replacement (not that MR wouldn't be helped with good data as well ...). Cheers Clemens -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
