PyMol

Tutorial
link (pdf)

Alignment

To align structure1 onto structure2, type:

align structure1, structure2

which will also report the RMSD value.


RMSD
RMSD = SQRT[{SUM(dii)2}/N] where dii is the distance between the ith atom of structure1 and the ith atom of structure2 and N is the number of atoms matched in each structure.

Show disulfide bonds on your cartoon
show sticks, (cys/ca+cb+sg)

Electron Density Maps

Download the .pdb from the RCSB PDB
Download the electron density map from the electron density server
    -use the CNS option with 2mFo-DFc, download and extract the *.cns and rename to *edm.xplor

the whole mesh can now be displayed, but it is better to use the following command to only generate the bits required:
(I was interested in C135 of 1T4B)

isomesh mesh, 1t4bedm, 1.0, /1T4B//B/CYS`135, 5.0

mesh is the name to be given to the new mesh
1t4bedm is the name of the file containing the electron density info
/1T4B//B/CYS`135 is the atom to centre the mesh around
5.0 is the angstrom size for the mesh box

or display the whole mesh and carve out the bits you want: link

Making Movies
link

Appearance
Sticks
set stick_radius=0.15, sele
will change the width of the selection only (0.25 is the default, can use set stick_width to return to default)

Windowsize
ray 1500, 1000
will produce a ray-traced image of 1500pixels wide, 1000pixels high.
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