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 File, Open 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