Displaying Biochemical Properties

Selecting secondary structures

A few examples:

 select helix, (ss h)
 select sheet, (ss s)
 select loop, (ss l+'')

Manually Assigning Secondary Structure

You can manually assign secondary stuctures to your protein by

 alter 96-103/, ss='S'
 alter 96-103/, ss='H'
 alter 96-103/, ss='L'

to set residues 96-103 to beta Strand, alpha Helix, and Loop respectively.

See Also

Dss Caver

FAQ Displaying Biochemical Properties

Color by atom type from a script

See Color for this.

Displaying double bonds

• 

  Image showing double bonds in PyMOL. Double bonds are supported in lines and sticks.

You can go into the lines mode and turning on the valence display:

hide
as lines
set valence, 0.1

A higher value for valence spreads things out more. I don't know of a way to get the dotted notation.

Calculating dihedral angles

The get_dihedral function requires four single-atom selections to work:

get_dihedral prot1///9/C, prot1///10/N, prot1///10/CA, prot1///10/C

Hydrogen bonds and Polar Contacts

Polar Contacts in PyMol

Using the actions [A] button for an object or selection you can display Hydrogen bonds and Polar Contacts. [A]->find->polar contacts-><select from menu>

The command behind the menus is the distance command called with the additional argument mode=2.

Parameters that control the the identification of H-bonds are defined as

set h_bond_cutoff_center, 3.6

with ideal geometry and

set h_bond_cutoff_edge, 3.2

with minimally acceptable geometry.

These settings can be changed *before* running the detection process (dist command mode=2 or via the menus).

Note that the hydrogen bond geometric criteria used in PyMOL was designed to emulate that used by DSSP.

Hydrogen bonds between specific atoms

dist name, sele1, sele2, mode=2

Hydrogen bonds where find->polar contacts doesn't do what you need

You can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use h_add on the proteins, or provide ligands with valence information and then use h_add.

Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens.

# EXAMPLE 1: Show hydrogen bonds between protein 
# and docked ligands (which must have hydrogens)

load target.pdb,prot
load docked_ligs.sdf,lig

# add hydrogens to protein

h_add prot

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (lig and acc),(prot and don), 3.2
dist HBD, (lig and don),(prot and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# EXAMPLE 2
# Show hydrogen bonds between two proteins

load prot1.pdb
load prot2.pdb

h_add prot1
h_add prot2

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (prot1 and acc),(prot2 and don), 3.2
dist HBD, (prot1 and don),(prot2 and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# NOTE: that you could also use this approach between two
# non-overlapping selections within a single object.

There is also a script drawing nice hydrogen bonds from Gareth Stockwell.

The "polar contacts" mentioned above are probably better at finding hydrogen bonds than these scripts. "Polar contacts" check geometry as well as distance.

Assign color by B-factor

See section Color for this.

Cavities

See Surfaces_and_Voids. Also Caver.

Surface Area

To calculate the surface area of a selection, see Get_Area.

Polar surface area

For a solvent accessible PSA approximation:

set dot_density, 3
remove hydro
remove solvent
show dots
set dot_solvent, on
get_area elem N+O
get_area elem C+S
get_area all

For molecular PSA approximation

set dot_density, 3
remove hydro
remove solvent
set dot_solvent, off
get_area elem N+O
get_area elem C+S
get_area all

Showing dots isn't mandatory, but it's a good idea to confirm that you're getting the value for the atom dot surface you think you're using. Please realize that the resulting numbers are only approximate, reflecting the sum of partial surface areas for all the dots you see. To increase accuracy, set dot_density to 4, but be prepared to wait...

Display solvent accessible surface

Using the surface display mode, PyMOL doesn't show the solvent accessible surface, rather it shows the solvent/protein contact surface. The solvent accessible surface area is usually defined as the surface traced out by the center of a water sphere, having a radius of about 1.4 angstroms, rolled over the protein atoms. The contact surface is the surface traced out by the vdw surfaces of the water atoms when in contact with the protein.

PyMOL can only show solvent accessible surfaces using the dot or sphere representations:

for dots:

show dots
set dot_mode,1
set dot_density,3

for spheres:

alter all,vdw=vdw+1.4
show spheres

Displaying the C-Alpha trace of proteins

hide
show ribbon
set ribbon_sampling,1

And if your model only contains CA atoms, you'll also need to issue:

set ribbon_trace,1

Displaying the Amino Acid Backbone

The easiest way to see the backbone of the protein is to do

hide all
show ribbon

If you don't like the ribbon representation, you can also do something like

hide all
show sticks, name C+O+N+CA

You can replace sticks in the above by other representations like spheres or lines.

Displaying the Phosphate backbone of nucleic acids

Native Nucleic Acid Rendering in PyMol

PyMol now better supports viewing nucleic acid structure. Nuccyl still seems to be the reigning champ for image quality, but see PyMol's native Cartoon command.

---

Should you ever want to show the phosphate trace of a nucleic acid molecule:

def p_trace(selection="(all)"):
    s = str(selection)
    cmd.hide('lines',"("+s+")")
    cmd.hide('spheres',"("+s+")")
    cmd.hide('sticks',"("+s+")")
    cmd.hide('ribbon',"("+s+")")
    cmd.show('cartoon',"("+s+")")
    cmd.set('cartoon_sampling',1,"("+s+")")
    cmd.set('cartoon_tube_radius',0.5,"("+s+")")
cmd.extend('p_trace',p_trace)

and then:

p_trace (selection)

Align proteins with CA fit

If two proteins have significant homology, you can use the Align command:

align prot1////ca,prot2

which will perform a sequence alignment of prot1 against prot2, and then an optimizing fit using the CA positions. I'm not sure if the help text for align got into 0.82, but the next version will definitely have it.