Displaying Biochemical Properties
- 1 Selecting secondary structures
- 2 Color by atom type from a script
- 3 Displaying double bonds
- 4 Calculating dihedral angles
- 5 Hydrogen bonds and Polar Contacts
- 6 Adding hydrogen bonds
- 7 Assign color by B-factor
- 8 Polar surface area
- 9 Display solvent accessible surface
- 10 Displaying the C-Alpha trace of proteins
- 11 Displaying the Amino Acid Backbone
- 12 Displaying the Phosphate backbone of nucleic acids
- 13 Align proteins with CA fit
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.
Color by atom type from a script
See Color for this.
Displaying double bonds
You can go into the lines mode and turning on the valence display:
hide show 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
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.
Adding hydrogen bonds
Regarding H-bonds. There isn't a built-in function yet, but 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 Cmd 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.)
Easy Hydrogen Bonds
dist name, sele1, sele2, mode=2
Assign color by B-factor
See section Color for this.
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:
show dots set dot_mode,1 set dot_density,3
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:
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
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)
Align proteins with CA fit
If two proteins have significant homology, you can use the Cmd align command:
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.