Electron Tomography Toolbox for Amira

ccp4read

Description:

The ccp4read module loads a CCP4 map density file, with the default extension .map. The file has to be in little endian byte ordering. Otherwise it can be loaded as raw format with a 1024 byte header (256 longs). The structure of a CCP4 map file is as follows:

1	NC	# of Columns (fastest changing in map)
2	NR	# of Rows
3	NS	# of Sections (slowest changing in map)
4	MODE	Data type 0 = envelope stored as signed bytes (from -128 lowest to 127 highest) 1 = Image stored as Integer2 2 = Image stored as Reals 3 = Transform stored as Complex Integer2 4 = Transform stored as Complex Reals 5 == 0 Note: Mode 2 is the normal mode used in the CCP4 programs. Other modes than 2 and 0 may NOT WORK
5	NCSTART	Number of first COLUMN in map
6	NRSTART	Number of first ROW in map
7	NSSTART	Number of first SECTION in map
8	NX	Number of intervals along X
9	NY	Number of intervals along Y
10	NZ	Number of intervals along Z
11	X length	Cell Dimensions (Angstroms)
12	Y length	Cell Dimensions (Angstroms)
13	Z length	Cell Dimensions (Angstrom)
14	Alpha	Cell Angles (Degrees)
15	Beta	Cell Angles (Degrees)
16	Gamma	Cell Angles (Degrees)
17	MAPC	Which axis corresponds to Cols. (1,2,3 for X,Y,Z)
18	MAPR	Which axis corresponds to Rows (1,2,3 for X,Y,Z)
19	MAPS	Which axis corresponds to Sects. (1,2,3 for X,Y,Z)
20	AMIN	Minimum density value
21	AMAX	Maximum density value
22	AMEAN	Mean density value (Average)
23	ISPG	Space group number
24	NSYMBT	Number of bytes used for storing symmetry operators
25	LSKFLG	Flag for skew transformation, =0 none, =1 if foll
26-34	SKWMAT	Skew matrix S (in order S11, S12, S13, S21 etc) if LSKFLG .ne. 0.
35-37	SKWTRN	Skew translation t if LSKFLG .ne. 0. Skew transformation is from standard orthogonal coordinate frame (as used for atoms) to orthogonal map frame, as Xo(map) = S * (Xo(atoms) - t)
38-52	future use	(some of these are used by the MSUBSX routines in MAPBRICK, MAPCONT and FRODO) (all set to zero by default)
53	MAP	Character string 'MAP ' to identify file type
54	MACHST	Machine stamp indicating the machine type which wrote file
55	ARMS	Rms deviation of map from mean density
56	NLABL	Number of labels being used
57-256	LABEL(20,10)	10 80 character text labels (ie. A4 format)

Map data follows.

How to use:

A file with the default extension .map can be loaded by just double clicking on the file in the open file dialog box. Files with another extension, which are in a CCP4 map format can be loaded by right clicking on the file in the dialog box and choosing Format from the popup menu. In the file format chooser select "CCP4 Density Map" and press OK. Press the Open Button in the open file dialog box.

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