PyMOL Wiki - User contributions [en]

Displaying Biochemical Properties

2009-05-16T17:40:07Z

Pablo.englebienne: /* Hydrogen bonds and Polar Contacts */ +link DSSP

==Selecting secondary structures==
A few examples:
<source lang="python">
select helix, (ss h)
select sheet, (ss s)
select loop, (ss l+'')
</source>

===Manually Assigning Secondary Structure===
You can manually assign secondary stuctures to your protein by
<source lang="python">
alter 96-103/, ss='S'
alter 96-103/, ss='H'
alter 96-103/, ss='L'
</source>

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

===See Also===
[[Dss]] [[Caver]]

[[:Category:FAQ|FAQ]] [[:Category:Objects_and_Selections|Displaying Biochemical Properties]]

==Coloring ==
See also [[:Category:Coloring]].

===Color by atom type from a script===
See [[Color]] for this.

===Assign color by B-factor===
See section [[Color]] for this.

== Bonds ==
PyMOL can deduce bonds from the PDB structure file, even if the '''CONECT''' records are missing. In fact, PyMOL guesses bonding connectivity based on proximity, based on the empirical observation that two atoms of a given radius will not be generally closer than a certain distance unless they are bonded.

===Displaying double bonds===
<gallery widths="300px" heights="300px">
Image:DoubleBonds.png|Image showing double bonds in PyMOL. Double bonds are supported in [[lines]] and [[sticks]].
</gallery>

You can go into the [[lines]] mode and turning on the valence display:
<source lang="python">
hide
as lines
set valence, 0.1
</source>

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

===Hydrogen bonds and Polar Contacts===
[[Image:Polar_contacts_small.png|thumb|Polar Contacts in PyMol|center|300px]]
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 <b>dist</b>ance 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 [http://swift.cmbi.kun.nl/gv/dssp/ DSSP].

==== Hydrogen bonds between specific atoms ====
<source lang="python">
dist name, sele1, sele2, mode=2
</source>

==== 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.
<source lang="python">
# 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
</source>
<source lang="python">
# 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.
</source>
There is also a [http://www.ebi.ac.uk/~gareth/pymol/downloads/scripts/hbond.py script] drawing nice hydrogen bonds from [http://www.ebi.ac.uk/~gareth 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.

==Calculating dihedral angles==
The get_dihedral function requires four single-atom selections to work:
<source lang="python">
get_dihedral prot1///9/C, prot1///10/N, prot1///10/CA, prot1///10/C
</source>

== Cavities ==
See [[Surfaces_and_Voids]]. Also [[Caver]] and [[CASTp]].

==Surface-Related==

===Surface Area===
To calculate the surface area of a selection, see [[Get_Area]].

===Polar surface area===
For a solvent accessible PSA approximation:
<source lang="python">
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
</source>

For molecular PSA approximation
<source lang="python">
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
</source>

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:
<source lang="python">
show dots
set dot_mode,1
set dot_density,3
</source>

for spheres:
<source lang="python">
alter all,vdw=vdw+1.4
show spheres
</source>

===Contact Potential===
See [[Protein_contact_potential]] and [[APBS]].
[[Image:Prot_contact_pot.png|thumb|right|125px]]
<div style="clear:right;"> </div>

===Residues with functional groups===
[[Image:1igt_cys_lys_asp_glu_colored.png|thumb|200px|Whole residues colored (Cys: yellow, Lys: blue, Asp and Glu: red)]]
Poor man's solution: Display protein as surface, colorize all Lys (-NH2), Asp and Glu (-COOH) and Cys (-SH):
<source lang="python">
remove resn hoh # remove water
h_add # add hydrogens

as surface
color grey90

color slate, resn lys # lysines in light blue
color paleyellow, resn cys # cysteines in light yellow
color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red
</source>

[[Image:1igt_functional_groups_colored.png|thumb|200px|Only central atoms of functional groups colored (Cys: S, Lys: NH2, Asp and Glu: CO2)]]
Not-''so''-poor-man's solution: In order to have the functional groups better localized, only the central atoms can be colored:
* the S atom of cystein,
* the N and H atoms of the free amine of lysine (may be displayed with three H atoms at all three possible positions)
* the C and two O atoms of free carboxylic groups in aspartic and glutamic acid
In this way, they are better visible through the surface compared to only one colored atom, both amines and carboxylic groups consist of three colored atoms each.
<source lang="python">
remove resn hoh # remove water
h_add # add hydrogens

as surface
color grey90

select sulf_cys, (resn cys and (elem C)) # get the sulfur atom of cystein residues
color yellow, sulf_cys

select nitro_lys, (resn lys and name NZ) # get the nitrogens of free amines ("NZ" in PDB file)
select hydro_lys, (elem H and (neighbor nitro_lys)) # get the neighboring H atoms
select amine_lys, (nitro_lys or hydro_lys)
color tv_blue, amine_lys

select oxy_asp, (resn asp and (name OD1 or name OD2)) # get the two oxygens of -COOH ("OD1", "OD2")
select carb_asp, (resn asp and (elem C and (neighbor oxy_asp))) # get the connecting C atom
select oxy_glu, (resn glu and (name OE1 or name OE2)) # oxygens "OE1" and "OE2" in PDB file
select carb_glu, (resn glu and (elem c and (neighbor oxy_glu)))
select carboxy, (carb_asp or oxy_asp or carb_glu or oxy_glu)
color tv_red, carboxy
</source>

By displaying the protein as non-transparent surface, only the functional groups (colored atoms) at the surface are visible. The visualization of those groups can be pronounced by displaying the corresponding atoms as spheres, e.g. "as spheres, carboxy + amine_lys + sulf_cys", in this way it might become more clear how accessible they are.

When displaying the protein as cartoon, the functional groups can be shown as spheres, and the whole residues cys, lys, asp and glu as sticks connected to the backbone, with the atoms of the functional groups again as spheres. However, then also the not accessible residues inside the protein are visible.

== Backbones ==
===Displaying the C-Alpha trace of proteins===
<source lang="python">
hide
show ribbon
set ribbon_sampling,1
</source>

And if your model only contains CA atoms, you'll also need to issue:
<source lang="python">
set ribbon_trace,1
</source>

===Displaying the Amino Acid Backbone===
The easiest way to see the backbone of the protein is to do
<source lang="python">
hide all
show ribbon
</source>

If you don't like the ribbon representation, you can also do something like
<source lang="python">
hide all
show sticks, name C+O+N+CA
</source>
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. For more information on representing nucleic acids, please see the [[:Category:Nucleic_Acids|Nucleic Acids]] Category.
[[Image:Cnam_0.png|right|thumb|130px]] <div style="clear:right;"> </div>

Should you ever want to show the phosphate trace of a nucleic acid molecule:
<source lang="python">
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)
</source>

and then:
<source lang="python">
p_trace (selection)
</source>

==Align proteins with CA fit==
If two proteins have significant homology, you can use the [[Align]] command:
<source lang="python">
align prot1////ca,prot2
</source>

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.

[[Category:Objects_and_Selections|Displaying Biochemical Properties]]
[[Category:Nucleic_Acids|Displaying Biochemical Properties]]
[[Category:Biochemical_Properties]]

Modeling and Editing Structures

2009-05-16T17:33:48Z

Pablo.englebienne: /* Adding hydrogen bonds */ +wikilink

=Modeling in PyMOL=

==Saving with transformed coordinates==

Here is a simple script that saves the molecule with coordinates from the current orientation.
(invoke it with 'run save_transformed.py' and type the new save_transformed.py command thereafter).
<source lang="python">
# Adds the command save_transformed
# Usage: save_transformed object, file
def save_transformed(object,file):
m = cmd.get_view(0)
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.transform_object(object,ttt)
cmd.save(file,object)

cmd.extend('save_transformed',save_transformed)
</source>

==Translate or rotate individual objects==
There is a "translate" function similar to "rotate", the docs for these don't exist yet, because the implementation isn't finished. However, feel free to use them in the following forms:

<source lang="python">
translate vector,object-name,state
(vector needs to be something like [x,y,z])

translate [1,0,0],pept

rotate axis,angle,object-name,state
(axis can be either the letter x,y,z or a 3D vector [x,y,z])
rotate x,90,pept
rotate [1,1,1],10,pept
</source>

==Moving one segment relative to the rest==

This means moving two parts of one object into different directions. The easiest way to do this is to split the objects and then use the rotate command.
<source lang="python">
load 1FJ1.pdb

# split PDB file

create anti=(chain F)
create fab=(chain A,B)

# delete original object
delete 1FJ1

# color objects
color green,fab
color pink,anti

# color interface
select inter = (byres ((fab within 5 of anti)\
or (anti within 5 of fab)))

color yellow,inter

# splay apart
orient
origin fab
rotate y,60,fab
origin anti
rotate y,-60, anti

# zoom interface region
zoom inter
show sph,inter
disable inter
</source>

==Split states to objects==
There is also a new command in the 0.95 series:
<source lang="python">
split_states object-name
</source>
which will spread a PDB "biological unit" (or any multi-state object -- including SD files) over a series of independent objects. This makes it possible to interact with such objects more naturally than with "all_states = 1".

==Altering secondary structures==

Examples:
<source lang="python">
alter A/10:34/, ss='H'
alter A/35:40/, ss='L'
alter A/41:60/, ss='S'
</source>

==Altering van der Waals radii==

Example:
<source lang="python">
alter (elem Fe),vdw=1.8
rebuild
</source>
(The value for Fe is wrecked in PyMOL at the moment, so running the above line might be a good idea).

==Altering atom coordinates==

Example:
<source lang="python">
alter_state 1,(pdb1cse),x=x-10.0
</source>
The latter section can contain formulae involving at least the xyz coordinates, lots of constants and the (+-*/) operators.

==Deleting bonds==

Select the bond using Ctrl-right-click, then either
<source lang="python">
unbond pk1,pk2
</source>
or hit Ctrl-D.

==Converting D- to L- amino acids==
The inversion function was changed in version 0.95 to take advantage of multiple picked atoms. To invert a center, Ctrl-middle-click to pick the center atom as pk1 and two stationary atoms as pk2 and pk3. Then type Ctrl-E to invert.

==Adding disulfide bonds==
You can use the [[Cmd bond]] command to attach them:
<source lang="python">
bond 24/sg,26/sg
bond 56/sg,99/sg
unpick
</source>
(unpick will hide the bond baton which gets displayed.)
Additionally, the residue names can be changed for bonded cysteines:
<source lang="python">
alter cys/,name='CYX'
</source>
or for specific residues
<source lang="python">
alter 24+26+56+99/,name='CYX'
</source>

==Adding hydrogen bonds==
:''See [[Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts|Displaying biochemical properties]].''

==Protonating ligands==
If your ligands come in with valid valencies and formal charges, PyMOL's h_add command can protonate ligands. (NOTE that there is a minor technical hiccup with SD-files which are loaded by default as immutable "discrete" objects.) Suffice it to say that in order to make changes to the chemical structure, an object must be loaded with the "discrete" flag set to zero.
Unfortunately, much of the molecular editing stuff remains to be documented. Here's an example sequence, but I'm not sure it will help to much...as indicated in the manual, this is immature functionality with some major gaps. Attach in particular is very limited...

<source lang="python">
# show valences
set valence=0.05

# load cysteine fragment
fragment cys

# remove hydrogens
remove (hydro)

# edit gamma S
edit cys////sg

# add hydrogen
attach H,1,1

# add planer, trivalent nitrogen onto C terminus
edit cys////C
attach N,3,3

# edit that nitrogen
edit (elem N and neighbor cys////C)

# attach a tetrahedral methyl (note random position)
attach C,4,4

# here's an example of adding a whole residue from the library
edit cys////N
editor.attach_amino_acid("pk1","ace")

# now restore missing hydrogens (note that the names are off...)
h_add
</source>

==Superposition of two molecules==
Using pair_fit requires that you specify a set of paired atoms in each structure. Fortunately, you no longer have to specify each pair separately, so long as the ordering is the same in each selection (almost always true).
<source lang="python">
pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and name P )
</source>

Another example:
<source lang="python">
pair_fit prot1///11-26/CA, prot2///34-49/CA
</source>
would superimpose prot1 on prot2 using C-alphas from residues 11-26 in prot1 and 34-49 in prot2.

==Manual superposition of two molecules==
You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.

Protect one object, deprotect the other, grab the deprotected object and move with Shift-Mouse.
Don't forget to switch to Mouse Editing mode.

==Adding and using your own fragments==
Pymol has some build-in fragments (amino acids and simple functional groups). You can add your own fragments, eg. sugars, in this way:

Create the molecule you want to use as a fragment. Save it as a .pkl file in <pymol_path>/data/chempy/fragments.

How to use the fragment:

Pick the atom (ctrl-middle) where you want to add the fragment. This will usually be a hydrogen atom (which will be removed). Then use the command:

editor.attach_fragment('pk1','my_fragment_name',11,0)

where my_fragment_name is the name of the pkl-file (w/o .pkl extension) and 11 is the number of the connecting (hydrogen) atom in the fragment.
To determine this number, press '[L]abel' -> 'atom identifiers' -> 'index' and choose the hydrogen atom you want.

If you want a hotkey for your fragment, you can probably put it in <pymol_path>/modules/pmg_tk/skins/normal/__init__.py, but I haven't tried this.

[[Category:Advanced Issues|Modeling and Editing Structures]]
[[Category:Biochemical_Properties]]
[[Category:States]]

Dash Gap

2007-02-07T19:35:13Z

Pablo.englebienne: added Category Settings, see also articles

== Overview ==
Sets the distance between dashes in labels.

== Syntax ==
<source lang="python">
set dash_gap, 0.1500
</source>

== Examples ==
<gallery>
Image:Dashes1000.png|Dash gap small -- dash_gap set to 0.1500
Image:Dashes3500.png|Dash gap normal -- dash_gap set to 0.3500
</gallery>

== See also ==
*[[Dash Length]]
*[[Dash Radius]]
*[[Dash Round Ends]]

[[Category:Settings]]

Dash Length

2007-02-07T19:34:01Z

Pablo.englebienne: added Category Settings, see also articles

== Overview ==
Sets the length of dashes in labels.

== Syntax ==
<source lang="python">
set dash_length, 0.3500 # make longer dashes
</source>

== Examples ==
<gallery>
Image:Dashes3500.png|Dash Length set to 0.1500
Image:Dl3500.png|Dash Length set to 0.3500
</gallery>

== See also ==
*[[Dash Gap]]
*[[Dash Radius]]
*[[Dash Round Ends]]

[[Category:Settings]]

Dash Radius

2007-02-07T19:33:53Z

Pablo.englebienne: /* See also */ added more dash-related articles

== Overview ==
Sets the width (radius) of the dashes.

== Syntax ==
<source lang="python">
set dash_radius, 0.500 # fat dashes
</source>

== Examples ==
<gallery>
Image:Dl3500.png|Normal size dashes
Image:Fat_dashes.png|Fat dashes; dash_radius set to 0.100
</gallery>

== See also ==
*[[Dash Gap]]
*[[Dash Length]]
*[[Dash Round Ends]]

[[Category:Settings]]

Dash Round Ends

2007-02-07T19:33:45Z

Pablo.englebienne: /* See also */ added more dash-related articles

== Overview ==
Sets roundness of the ends of label dashes.

== Syntax ==
<source lang="python">
set dash_round_ends, 0 # square ends
</source>

== Examples ==
<gallery>
Image:Fat_dashes.png|Rounded dash-ends
Image:Dash_square_ends.png|Squared off dash-ends
</gallery>

== See also ==
*[[Dash Gap]]
*[[Dash Length]]
*[[Dash Radius]]

[[Category:Settings]]

Dash Round Ends

2007-02-07T19:31:02Z

Pablo.englebienne: added Category Settings, see also articles

Dash Radius

2007-02-07T19:30:53Z

Pablo.englebienne: added Category Settings, see also articles

Dash radius

2007-02-07T19:29:53Z

Pablo.englebienne: redirect to Dash Radius

#REDIRECT [[Dash Radius]]

Sphere scale

2007-02-07T19:01:48Z

Pablo.englebienne: added Category Settings

==Overview==

This setting affects the apparent radius of spheres in the sphere representation. Default scale is set to 1.0.

==Syntax==

set sphere_scale, ''size''

''size'' can be any float number. Using 0.25 gives a nice balls&sticks representation with both lines and spheres turned on.

set sphere_scale by itself will revert to default.

==Related settings==
*[[sphere_color]]
*[[sphere_mode]]
*[[sphere_point_max_size]]
*[[sphere_point_size]]
*[[sphere_quality]]
*[[sphere_solvent]]
*[[sphere_transparency]]

[[Category:Settings]]

Stick radius

2007-02-07T18:43:29Z

Pablo.englebienne: created initial description, based on sphere_scale

==Overview==

This setting affects the radius of sticks in the sticks representation. Default scale is set to 0.25.

==Syntax==

<code>set sticks_radius, ''size''</code>

''size'' can be any float number. Using 0.25 (default value) is usually appropriate for most representations, although 0.15 migh be preferred for comparing closely related structures, e.g., conformers.

''Note:'' <code>set stick_radius</code> by itself will revert to 1.00.

==Related settings==

*[[sphere_scale]]
*[[stick_ball_ratio]]