Dear chimera team, I've found the map segmentation tool very useful. However I would like to split the map according to the segments. Is it possible to do that? Thanks in advance! Best regards, Gabor ----------------- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748
Dear Gabor, I don't know of a single step to create separate maps for all the separate segmentation regions, but below is how to do it for one region at a time. You can use the "mask" command to extract the data within some surface, such as from segmentation. For example, if the original volume data is model #0 and you selected (Ctrl-click in graphics window) the segmentation surface of interest, the command could be something like: mask #0 sel ... which would create a new volume model. The mask command has several options, such as for inverting what you get or extracting a slab around the surface, see: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> There is also a "segment" command with "exportmask" option to create a map in which the values are the identifiers of the segmentation regions: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/segment.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 21, 2011, at 5:04 AM, Gabor PAPAI wrote:
Dear chimera team, I've found the map segmentation tool very useful. However I would like to split the map according to the segments. Is it possible to do that? Thanks in advance! Best regards, Gabor
Hi Gabor, The File / Save Each Region to .mrc File menu entry of the Segment Map dialog creates a separate map for each selected segmentation region and saves those maps to files. If you don't select any regions then all of them will be used. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html... When you mask maps to regions it is helpful if the regions were created using a lower contour level than what you intend to use for display. If instead you create the regions with the contour level you want to display at then the masking creates ugly stair-step artifacts at that contour level because the map has been set to zero right outside that level. Using a lower contour level for creating the regions gives bigger regions that alleviates this problem. Tom
Dear chimera team,
I've found the map segmentation tool very useful. However I would like to split the map according to the segments. Is it possible to do that? Thanks in advance!
Best regards,
Gabor
----------------- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748
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participants (3)
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Elaine Meng -
Gabor PAPAI -
Tom Goddard