Ok, Graeme basically described the way I usually do things as well. That's the beauty of a modular program like XDS and the passing of information in ASCII format. Old-fashioned, but very, very useful ;-)
I've created a short page with a recipe for using XDS in that way - there might be some typos still in there, but it might give you the idea: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Indexing Cheers Clemens On Mon, Feb 18, 2008 at 01:43:43PM -0000, Winter, G (Graeme) wrote: > 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: [email protected] > 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) > *************************************************************** > -- *************************************************************** * 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) ***************************************************************
