Pymol

The current version is 0.88 or 1.8.3.2 on Mac
The files are in /home/bio/pymol
You run it by  /home/bio/Bin/Pymol
Home page: http://pymol.sourceforge.net/
There is also a commercial variant by Schrödinger.

Pymol is a program to visualise structures, including electron density maps. It has great graphics.


General Use

1.     Before you load the pdb file, it is wise to make sure that atoms you will work on have correct residue names (not all “1”), and that it contains all atoms you need.

2.     Load the all_pdb.pdb file (.pdb extension is necessary):
command pymol all_pdb.pdb  in the shell or
command  pymol , then FileOpen in the window 

3.     Add bond: In the PyMOL Viewer window, right down corner, click Mouse Mode to 3-Button Editing condition, click on two atoms, then command bond (unbound to disconnect).

4.     Make new selection: click on Mouse Mode, under the 3-Button Viewing mode, you (click on) Selecting by Atoms, Residues, Chains, Segments, Objects, Molecules, C-alpha; Click on residues or atoms you will work on, then you get a new selection (shown at the right column, with a default name sele). You may want to name it as target_pdb by the button A next to it, then rename selection or use command set
set_name old_name, new_name

5.     Making new selection is useful if you do not want to show all atoms inside all_pdb. You can select residues that would be shown in the figure as a new selection and hide other atoms (all_pdb) by the commands
hide (all_pdb)
show_as stick, target_pdb


6.     Background: (bg_rgb) can be set to white; set Transparent Background; Turn off shadows, depth cueing, reflections (useful for printing on normal paper or in thesis).

7.     Color:  color command + color_name + element_name. color_name can be found at the right side of the pymol window “C” key, usually those are enough.

8.     The structure can be shown in stick model, show_as stick, all (or a certain selection you want). Use stick_radius to set the bond thickness; 

bg_color white
set show_alpha_checker , on;
set ray_opaque_background, off;  
set ray_shadows,0; 
set specular, off
set depth_cue, 0

color gray70, (name C*) ;   color yellow, (name S*) ; color cyan, (name M*) ; color orange, (name F*) ;  color red,(name O*);   color blue, (name N*);color magenta, (name V*);color white,(name H);

show_as stick, target_pdb ; set_bond stick_radius, 0.1, target_pdb
set valence, 0



Maps

1.     Load  the Fo–Fc and Fo–Fc maps in ccp4 format.
You can rename them as fo_fc and 2fo_fc          

set mesh_width, 0.25
isomesh fm, fo_fc, -3.0,  target_pdb,
isomesh fp,  fo_fc,   3.0, target_pdb,
isomesh 2f,  2fo_fc, 1.0, target_pdb

 

2.     Color positive map green and negative red.

3.     Depending on the quality of structure, you may also want to change carve. If "carve" is not provided, then the whole brick is displayed.
For example,
isomesh 2f,  2fo_fc, 1.0, target_pdb, carve=2.2  
means that you only show densities within 2.1 Å of atoms

4.     Save as picture.  (the size of the picture should decrease when the picture contains much information)

ray 2400, 2400

png  path/fig_name




Colour-code atoms according to b-factors

spectrum b, blue_white_red, minimum=20, maximum=50


Installation on Mac (27/9-16)

sudo port install tcl -corefoundation
sudo port install pymol

(The first command was needed, because otherwise the installation failed)