Hi Sergei, I don't think that there is a program available to do what you want, but I think that the tools are there for you to make one. The biggest challenge you will have is keeping the mathematics straight!
So, if you start off with something like the DiffractionImage library, this will help with reading in the diffraction images - contact Francois Remacle for this one ([EMAIL PROTECTED]) - you will need to know the beam centre, wavelength and detector distance *exactly* for this to be useful. Well, more exactly than is normal in image headers ;o) Next you will need something which can render the 3D density that you will generate - I would google "voxel" and see what you can come up with. I vaguely remember some libraries for this kind of thing available in C/C++. Common uses are medical imaging. Now comes the tricky bit. You will need to work through each image and for each pixel add the approptiate constant times the pixel value to the "right" voxel given by the diffraction geometry. The calculations for this appear in most crystallography texts, though I expect computing said constant will be non-trivial. The constant will correct for the "volume" of the pixel in reciprical space, determined by the position on the detector face and the oscillation angle. After that you should be about done. Oh, and you might want to do this on rather a large computer if you intend to get a high resolution representation of each reflection on all of the images. If you are wanting a voxel cube 1000 pixels to a side (say) as int*2 (say) this is a 2GB before you have read in your first image. Without some kind of prediction and shoeboxing (as goes on inside XDS, for instance) you won't be able to avoid this. Good luck, Graeme -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sergei Strelkov Sent: 12 July 2007 16:29 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Program to 'visualize' the reciprocal space ? Many thanks to good people who have responded to my message! Apparently I have to apologize for not formulating my question clearly enough. Here is more explanation. According to Ewald construction, diffraction images collected by oscillation method correspond to thin 'curved' slices of the reciprocal space. What I am looking for is a program to generate the reciprocal space (as a 3D map) from these 'slices' directly, *without* any indexing or integration of I's. This is a simple purely geometrical calculation. This is *not* anything routinely done for normal high-quality crystal data. For a good dataset, such a conversion should simply yield a lattice with distinct points. For our partially-ordered crystals, this should help us visualizing the actual 'shapes' of our reflections (many of them are smeared/overlapping). My guess that folks working with semi-ordered systems, such as liquid crystals or lipid bilayers, should have some programs like that... any ideas? Thank you again, Sergei. > Dear All, > > we are dealing with a difficult case of a 'partially ordered' protein > crystal. > Here it would be very useful to view the reciprocal space as a 3D map. > Is anyone aware of a program that would convert standard oscillation > data (one-degree frames, mar225) into such a map? What we need is a > direct conversion. > There is a program in CCP4 that is able to 'visualize' the reciprocal > space, but it requires hkl's as input. > > Thank you, > Sergei Strelkov > -- Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of Pharmaceutical Sciences, Catholic University of Leuven Campus Gasthuisberg, O&N2 Herestraat 49 bus 822, 3000 Leuven, Belgium Work phone: +32 16 33 08 45 Fax: +32 16 32 34 69 Mobile: +32 486 29 41 32 E-mail: [EMAIL PROTECTED] Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
