Crystallography‎ > ‎Molecular graphics‎ > ‎Pymol‎ > ‎

Electron Microscopy (EM) maps

If one has an EM map in .mrc format, she needs first to convert this in .ccp4 format.

Use map2map for the conversion, by typing:

map2map input.mrc output.ccp4

This will print a menu, where selecting 0 (zero) gives the classic menu with options (7 and 8) for the conversion of .mrc files to .ccp4:

map2map> Input map in MRC or CCP4 binary format detected.
map2map> Choose one of the following options (or 0 for classic menu):
map2map> 
map2map>      1: Wash self (auto)*
map2map>      2: Wash self or edit header (manual)**
map2map>      3: Convert to SPIDER binary* 
map2map>      4: Convert to X-PLOR (ASCII editable text)* 
map2map> 
map2map>      *: automatic fill of header fields 
map2map>     **: manual assignment of header fields 
map2map> 
map2map> Enter selection: 0
map2map> Entering classic map2map menu.
map2map> Select one of the following options:
map2map> 
map2map> Convert selected INPUT formats to Situs or MRC/CCP4*: 
map2map> 
map2map>      1: ASCII (editable text) file, sequential list of map densities** 
map2map>      2: MRC or CCP4 binary (auto)** 
map2map>      3: MRC or CCP4 binary (manual)*** 
map2map>      4: SPIDER binary*** 
map2map>      5: X-PLOR map (ASCII editable text)** 
map2map>      6: Generic 32-bit binary (unknown map or header parameters) 
map2map> 
map2map> Convert Situs or MRC/CCP4**** to one of these OUTPUT formats: 
map2map> 
map2map>      7: MRC / CCP4 binary (auto)**
map2map>      8: MRC / CCP4 binary (manual)***
map2map>      9: SPIDER binary** 
map2map>     10: X-PLOR (ASCII editable text)** 
map2map> 
map2map>      *: output format based on file extension (Situs if .sit or .situs, else MRC/CCP4)
map2map>     **: automatic fill of header fields
map2map>    ***: manual assignment of header fields
map2map>   ****: input format will be automatically detected, either Situs or MRC/CCP4
map2map> 
map2map> Enter selection: 7

After selecting 7, the program prints the following (pasting it here just for completeness and clarity):

lib_vio> Reading header information from MRC or CCP4 file input.mrc 
lib_vio>       NC =      300  (# columns)
lib_vio>       NR =      300  (# rows)
lib_vio>       NS =      300  (# sections)
lib_vio>     MODE =        2  (data type: 0: 8-bit char, 2: 32-bit float)
lib_vio>  NCSTART =     -150  (index of first column, counting from 0)
lib_vio>  NRSTART =     -150  (index of first row, counting from 0)
lib_vio>  NSSTART =     -150  (index of first section, counting from 0)
lib_vio>       MX =      299  (# of X intervals in unit cell)
lib_vio>       MY =      299  (# of Y intervals in unit cell)
lib_vio>       MZ =      299  (# of Z intervals in unit cell)
lib_vio> X length =  299.000  (unit cell dimension)
lib_vio> Y length =  299.000  (unit cell dimension)
lib_vio> Z length =  299.000  (unit cell dimension)
lib_vio>    Alpha =   90.000  (unit cell angle)
lib_vio>     Beta =   90.000  (unit cell angle)
lib_vio>    Gamma =   90.000  (unit cell angle)
lib_vio>     MAPC =        1  (columns axis: 1=X,2=Y,3=Z)
lib_vio>     MAPR =        2  (rows axis: 1=X,2=Y,3=Z)
lib_vio>     MAPS =        3  (sections axis: 1=X,2=Y,3=Z)
lib_vio>     DMIN =    0.000  (minimum density value - ignored)
lib_vio>     DMAX =    0.397  (maximum density value - ignored)
lib_vio>    DMEAN =    0.002  (mean density value - ignored)
lib_vio>     ISPG =        0  (space group number - ignored)
lib_vio>   NSYMBT =        0  (# bytes storing symmetry operators)
lib_vio>   LSKFLG =        0  (skew matrix flag: 0:none, 1:follows)
lib_vio>  XORIGIN = -178.219  (X origin - MRC2000 only)
lib_vio>  YORIGIN = -240.315  (Y origin - MRC2000 only)
lib_vio>  ZORIGIN =  -92.241  (Z origin - MRC2000 only)
lib_vio>      MAP =      MAP  (map string)
lib_vio>   MACHST = 68 68 0 0 (machine stamp - ignored)
lib_vio>      RMS =    0.000  (density rms deviation -ignored)
lib_vio> Volumetric data read from file input.mrc
lib_vio> C,R,S = X,Y,Z (no axis permutation). 
lib_vio> Using MRC2000 style origin defined by [X,Y,Z]ORIGIN fields.
lib_vio> Cubic lattice present. 
lib_vio> Input grid not in register with origin of coordinate system.
lib_vio> 
lib_vio> Writing MRC / CCP4 (binary) volumetric map 
lib_vio> Volumetric map written to file output.ccp4 
lib_vio> Header information: 
lib_vio>       NC =      300  (# columns)
lib_vio>       NR =      300  (# rows)
lib_vio>       NS =      300  (# sections)
lib_vio>     MODE =        2  (data type: 0: 8-bit char, 2: 32-bit float)
lib_vio>  NCSTART =        0  (index of first column, counting from 0)
lib_vio>  NRSTART =        0  (index of first row, counting from 0)
lib_vio>  NSSTART =        0  (index of first section, counting from 0)
lib_vio>       MX =      300  (# of X intervals in unit cell)
lib_vio>       MY =      300  (# of Y intervals in unit cell)
lib_vio>       MZ =      300  (# of Z intervals in unit cell)
lib_vio> X length =  300.000  (unit cell dimension)
lib_vio> Y length =  300.000  (unit cell dimension)
lib_vio> Z length =  300.000  (unit cell dimension)
lib_vio>    Alpha =   90.000  (unit cell angle)
lib_vio>     Beta =   90.000  (unit cell angle)
lib_vio>    Gamma =   90.000  (unit cell angle)
lib_vio>     MAPC =        1  (columns axis: 1=X,2=Y,3=Z)
lib_vio>     MAPR =        2  (rows axis: 1=X,2=Y,3=Z)
lib_vio>     MAPS =        3  (sections axis: 1=X,2=Y,3=Z)
lib_vio>     DMIN =    0.000  (minimum density value)
lib_vio>     DMAX =    0.397  (maximum density value)
lib_vio>    DMEAN =    0.002  (mean density value)
lib_vio>     ISPG =        1  (space group number)
lib_vio>   NSYMBT =        0  (# bytes used for storing symmetry operators)
lib_vio>   LSKFLG =        0  (skew matrix flag: 0:none, 1:follows)
lib_vio>  XORIGIN = -178.219  (X origin - MRC2000 only)
lib_vio>  YORIGIN = -240.315  (Y origin - MRC2000 only)
lib_vio>  ZORIGIN =  -92.241  (Z origin - MRC2000 only)
lib_vio>      MAP =      MAP  (map string)
lib_vio>   MACHST = 68 65 0 0 (machine stamp)
lib_vio>      RMS =    0.021  (density rmsd)
lib_vio> Input grid not in register with origin of coordinate system.
lib_vio> The origin information was saved only in the MRC2000 format fields.
lib_vio> The CCP4 start indexing was set to zero.
lib_vio> To invoke a crystallographic CCP4 indexing, you can force an interpolation 
lib_vio> by converting to an intermediate X-PLOR map using the map2map tool. 
map2map> 
map2map> All done.

Open now the newly generated output.ccp4 file in pymol, using simply the command 

load output.ccp4
 
This will generate the object "output", and clicking on the "A" (Action) menu on the pymol window one can now select to visualize the map as mesh, surface, slice, and so on.