Home > Pymol > Electron density map Refmac5

This is a method to convert the electron density (.mtz file) output by REFMAC5 and display it in PyMOL. Please have the PDB file and MTZ file output by REFMAC ready.

Launching FFT

Click "Run FFT - Create Map" in the "Map & Mask Utilities" submenu.



Run FFT

Set it as follows and click "Run".
  1. Select "all atoms in PDB file"
  2. Select MTZ file
  3. 2For Fo-Fc maps, change "F1" and "PHI" to "FWT" and "PHWT", respectively (for Fo-Fc maps, change "F1" and "PHI" to "DELFWT" and "PHDELWT", respectively)
  4. Select PDB file
  5. Change the extension of the Map out file to .ccp4



PyMOL

Open PDB file and CCP4 file with PyMOL. Please see Electron Density Map PDB for loading the electron density map.


Refine the mesh

If you draw a map without changing the settings, the mesh will look something like this.

Let's try making the mesh grid smaller.
  1. Double-click the completed FFT job in the CCP4 main window to open the log.
  2. Check the "Grid sampling on x, y, z" values ​​at the bottom of the log. In this example, x=96, y=168, z=180.



  3. Open FFT and in "Infrequently Used Options" enter a value that is a multiple of the "Grid sampling on x, y, z" checked in the log. The larger the value, the finer the grid will be. In this example, I doubled all the values.




Similarly, if you draw a map using PyMOL, it will look like this.


Please note that the finer the grid, the larger the file size will be. In this case, by doubling the grid value, the file size increased from 11.8MB to 94.0MB.