how to open density map by pymol(2 for xplor format)

1. covert the mtz to xplort. use phenix.FFT


2 http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html
1. Loading PDB file
File -> Open -> 1w2i.pdb

2. Load the map file
File -> Open -> 2fofc.map.xplor
It takes a while to load the map file.

3. Zoom in the active site
PyMOL> select active, (resi 14-20,38) and chain A
PyMOL> zoom active
PyMOL> hide all
PyMOL> show stick, active

4. Locate and Display the active site water
We know that the amide group of Asn38 is h-bond to an active water.
PyMOL> select active_water, ( (resi 38 and name ND2 and chain A) around 3.5) and (resn HOH)
The above command select any water molecules that is/are around 3.5A of the ND2 atom of resi 38 in chain A
PyMOL> show spheres, active_water
Well the Oxygen atom is now shown in its vdw radius. We can reduce the size of the sphere to 0.5A by:
PyMOL> alter active_water, vdw=0.5
PyMOL> rebuild

5. Display the electron density around the active site atoms at sigma level=1.0
PyMOL> isomesh mesh1, 2fofc.map, 1.0, (resi 14-20,38 and chain A), carve=1.6
Because the residue atoms were previously defined as "active", you can simply type:
PyMOL> isomesh mesh1, 2fofc.map, 1.0, active, carve=1.6

6. You can change the color of the map by:
PyMOL> color grey, mesh1

7. Normally you want to set the background color to white for publication
PyMOL> bg_color white

8. Publication quality figures
To render a figure with the default resolution (640x480)
PyMOL> ray
You will be able to preview the low resolution figures on screen. If you have done everything right, you should be able to see this:



To render a figure with high resolution
PyMOL> ray 2400,2400
Well, it takes a while to produce it. Then you can save the figures in PNG by
File -> Save Image

9. You can save the session by:
File -> Save Session
The saved session will be a .pse extension. You can reload it by double-click the .pse file in Windows.