[ccp4bb] superimposing Mtz maps
Hi, I have two maps from two different crystals with the same space group, both show an unknown density in the same place. I wanted to superimpose the maps to see if it is the same/similar density. Any ideas how to do this ? Thank you, Regards Rana
Re: [ccp4bb] superimposing Mtz maps
COOT can help you. If you have coordinates in both crystals COt can superpose the coordinates ( LSQ superpose) and carry the density with the coordinates. see under COOT extensions maps Transform maps by LSQ model fit Eleanor Rana Refaey wrote: Hi, I have two maps from two different crystals with the same space group, both show an unknown density in the same place. I wanted to superimpose the maps to see if it is the same/similar density. Any ideas how to do this ? Thank you, Regards Rana
Re: [ccp4bb] superimposing Mtz maps
Hi Rana, You could use cphasematch to put the two maps on the same origin. To do this you will need to CAD the two data sets together then give cphasematch the phase columns to use. Typing cphasematch on the command-line should tell you how to do this. It's a tool from the clipper library, so there is probably also a GUI for it in CCP4i. Cheers, Graeme 2009/7/21 Rana Refaey dr_r...@hotmail.com: Hi, I have two maps from two different crystals with the same space group, both show an unknown density in the same place. I wanted to superimpose the maps to see if it is the same/similar density. Any ideas how to do this ? Thank you, Regards Rana
Re: [ccp4bb] superimposing Mtz maps
This sounds a little like multi-crystal averaging without the averaging. If you were using the Uppsala program suite, you could perhaps do the following: [define one xtal as reference, the other as target] 1. Make mask in map grid for reference xtal (program MAMA) 2. Establish operator for reference - target transformation e.g. from protein superimposition with LSQMAN 3. Improve this operator for the two density maps (program MAVE) * do not average the maps, which would otherwise be the usual step 4. Expand the reference map into the target xtal, by lying to MAVE that the reference map is the averaged map. (program MAVE) There also appears to be an EZ skewing option in MAVE. Make sure you make the mask around the unknown density large enough so that MAVE/Improve has some density to work with for optimization that isn't just the unknown blob. You could always use a larger mask for this step and a smaller one for the MAVE/Expand step. Phil Jeffrey Princeton Rana Refaey wrote: Hi, I have two maps from two different crystals with the same space group, both show an unknown density in the same place. I wanted to superimpose the maps to see if it is the same/similar density. Any ideas how to do this ? Thank you, Regards Rana
Re: [ccp4bb] superimposing Mtz maps
Rana Refaey wrote: Hi, I have two maps from two different crystals with the same space group, both show an unknown density in the same place. I wanted to superimpose the maps to see if it is the same/similar density. Any ideas how to do this ? Thank you, Regards Rana Hi, you might want to try out Chimera. http://www.cgl.ucsf.edu/chimera/ The program has a very nice function to fit maps onto each other. We used Chimera to overlay two maps for our recent paper http://pubs.acs.org/doi/abs/10.1021/bi802320q Have a look on figure 6B. Best wishes, Tim -- Tim Schulte Ruhr-Universität Bochum LS Biophysik AG Proteinkristallographie Universitätsstr. 150 44780 Bochum Germany Tel. +49-234-32-25754
