Hi Gabor, Chimera currently has no way to fit one EM map into another EM map other than placing the map by hand. We plan on adding a local optimization capability for fitting one map in another-- it is almost the same code as the "fit models in maps" tool only the map-map correlation is optimized. This is probably less than a day's work to make the code changes but I am working on a grant right now and will not be able to look at it until next Thursday. If you can wait, I might be able to provide some code to test out at the end of next week. Tom

Hi Gabor, I added a dialog to Chimera for fitting one density map in another density map. Here is the code https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmapinma... The fitmapinmap.zip archive contains two directories FitMap and VolumeViewer that replace those in your Chimera distribution in chimera/share. I've tested this code with Chimera version 1.2309 (most recent snapshot). Installing the above code will create a new menu entry Tools / Volume Data / Fit Map in Map that shows the new dialog. You open the two maps using Chimera menu entry File / Open, then choose these maps in the fit map dialog and press the Fit button. This code does oly a local optimization so you have to position one map at approximately the right position in the other map before you optimize. It is very similar to the "Fit Models in Maps" tool distributed with Chimera that fits atomic models into maps. Use the Model Panel (menu entry Favorites / Model Panel) to freeze (switch active button off) one map and move the other map with the mouse. After pressing the Fit button the first map is rotated and shifted to increase the "overlap". The overlap is defined as the sum over the pointwise product of the two maps with given relative orientation. By default the sum is carried out over the grid points in the first map that are above the displayed contour level. The correlation of the two maps is the overlap divided by two normalization factors, the squareroot of the sum of squares of map values at the grid points for each map. If the values of the two maps at the grid points are represented as vectors u and v then in mathematical terms overlap = (u,v) correlation = (u,v)/|u||v| (= cosine of angle between vectors) where (u,v) means inner-product of vectors u,v and |u| means norm of u. The correlation is always in the range [-1,1] while the range of overlap values depends on the scaling of the maps. Optimizing the overlap is not the same as optimizing the correlation. I may add an option in the future to optimize correlation. The resulting position of one map in the other is given in the Reply Log (menu entry Favorites / Reply Log) as a 3 by 4 matrix (3x3 rotation matrix and the last column is a translation). Also the size of the shift and rotation angle is listed so you can get an idea about convergence. If you turn off the switch "Use only data above contour level from first map" then the set of grid points used includes all grid points of the first map having non-zero data values. The contour level is ignored. But points with data value = 0 (probably masked out in processing the map) are not used for the fit. By pressing the Correlation button (instead of the Fit) button you can get the correlation and overlap for the current map positions without moving either map. I encountered a bug in the Chimera gradient calculation code when interpolating values near the boundary of a map. It caused Chimera to crash when fitting a map in an identical copy of itself. I have fixed this bug, but the fix is in C++ code and is not included in the above zip archive. I don't think you will hit this bug when fitting a map in another map of differing size. This fit map in map tool and the bug fix will be in the next Chimera snapshot. I observed that sometimes I need to press the Fit button a second or third time to get convergence to the best fit. The fitting will make at most 100 gradient descent steps, but sometimes it decides it has converged even before then even though it is not yet at a locally optimal solution. The dialog does not give control over the convergence criteria (which is the same as the Fit Models in Maps tool) although in the future I may add access to these settings. Set the Fit Models in Maps documentation in the Chimera User's Guide for details on the method. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodels... Documentation for this Fit Map in Map tool is not yet available other than this description. Suggestions welcome! I'll be off for Thanksgiving until Monday. Tom