Hi Alex, The pixel size is in the MRC file header. It is (CELLA[0]/mx, CELLA[1]/my, CELLA[2]/mz). Refer to the MRC file documentation for details. http://www2.mrc-lmb.cam.ac.uk/image2000.html There is a file header word MACHST used to distinguish big-endian from little-endian files (value 0x11 0x11 0x00 0x00 or 0x44 0x44 0x00 0x00). Chimera does not use that. I think the reason is that it is not always set. In fact Chimera did not set it correctly when writing MRC files until just yesterday. Instead Chimera looks at the number of map columns (NC) and chooses the byte order that makes that value between 1 and 65536. For more details of reading MRC files see the Chimera python code in your distribution chimera/share/VolumeData/mrc/mrc_format.py On Mac the share directory is Chimera.app/Contents/Resources/share. Tom
Hi Tom, Elaine
Thanks for your replies - very helpful!
I followed one of the links from Elaine's email: http://ami.scripps.edu/prtl_data/mrc_specification.htm
Does this actually mean that pixel size is not provided in MRC file? Could you also perhaps comment on how chimera recognizes the density files with inverted order of bytes?
Thanks in advance Alex
Quoting "Tom Goddard" <goddard@sonic.net>:
Hi Alex,
Chimera reads the voxel size and map grid size from the headers of each of the volume file formats it reads. Often the correct voxel size is not given in the files and is set to 1.0. If it the file has zero (or negative) for the voxel size than Chimera uses of size of 1. You can change the voxel size within Chimera using the volume dialog Coordinates panel. Then you can save a new file with the volume dialog File / Save Map As... menu entry.
Tom
Hallo
Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file?
Thanks in advance Alex
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