Pymol操作命令

基本命令（也可使用鼠标操作，但不如命令来得简单）

pwd          # show current directory

dir          # list file in the current directory

cd directory #change directory 

load xxx                #注意要打上扩展名，例如1LMK.pdb，否则会errorc

reat name, (selection) #name=object to creat, selection=atom to include in the new object,非常实用的功能

Manipulating object:

show representation, (selection)

hide representation, (selection)

#the available representations are: (前面是个人比较常用的)lines, spheres, ribbon, cartoon, sticks, surface, /// mesh, dots, labels, extent

例如： stick mol1 & resi 100    # mol1为显示在pymol右边的分子名称

Turn an object on and off:(这个直接用鼠标就ok了)

enable/disable, object-name #turn on/off all representation

Basic atom selections:

name    缩写 n.<>         例子：  show cartoon, (n. 1LDK/)

resn       r.<>                   

resi      i.<>

chain           c.<>

elem      e.<>

Selection algebra:就是怎么选择

交集是and、&，例如 1LDK and chain A and i. 1-103

并集是or/|，补集是not/!

Change your point of view:

zoom, (selection)  #fit the selection to screen

orient, (selection)  #align molecular axisc

enter, (selection) # size not changed

turn axis, angle #rotate camera

move axis, distance  #translate camera

Align (个人认为最重要的功能)：

align (source), (target)   #the source object will be moved and rotated to fit the target object

例如： align (prot1 and chain A), (prot2 and chain B)  按整条链叠合

align mol1 & resi N1, mol2 & resi N2  按某一个残基叠合

align mol1 & resi N1-N2 & name n+ca+c+o，mol2 & resi N3-N4 & name n+ca+c+o 按某段残基的主链进行叠合

在align的过程中会产生一个root mean square deviation (RMSD),这个值可在一定程度上衡量alignment的效果。

Set control (可以通过这个命令来调整所有参数的值，可惜没有什么详细的介绍)

例如 set sphere_scale, 0.5, (n. Fe) #decrease Fe atom size to 0.5

set bg_rgb, [1,1,1] #set background as white

set ribbon_sampling, 1

Measurement (又一个十分重要的功能，可以真正挖掘结构的意义)

dist     #测量两个原子之间的距离，ctrl+右键选择第一个原子，ctrl+中键选择第二个原子，然后测量dist。

angel    # 测三个原子之间的夹角， ctrl＋中键选择第三个原子，然后测量angle

dihedral #测量四个原子之间的二面角

Launching PyMOL

• File for startup commands
• Launching PyMOL from an external program
• Running PyMOL in batch mode
• Suppressing PyMOL output
• Launching Python programs

 

 

File for startup commands

Linux:
Whenever PyMol starts, a '.pymolrc' file containing commands is run. All you need to do is create ".pymolrc" and place it in your home directory. Alternatively, you can instead create ".pymolrc.py" which contains actual Python code instead of just PyMOL commands.

Windows:
On Windows, use 'pymolrc', 'pymolrc.py' or 'pymolrc.pym'.

Warren DeLano

 

Launching PyMOL from an external program

If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you can launch PyMOL from an external Python program as shown inexamples/devel/start_pymol.py.

NOTE: This approach is not recommended, since the PyMOL launching process is subject to change without warning. The recommended approach is to just use PyMOL as your python interpreter:

pymol -r

pymol -qcr

Warren DeLano

 

Running PyMOL in batch mode

To perform PyMOL commands from stdin (file, pipe) without opening an OpenGL window, try:

pymol -qc

 

Suppressing PyMOL output

Just type:

feedback disable,all,actions

feedback disable,all,results

-From Python:

cmd.feedback("disable","all","actions")

cmd.feedback("disable","all","results")

Will suppress most of PyMOL's normal chatter.

 

Launching Python programs

Running a Python script from PyMOL, usually the command:

run script.py

Is enough. Of course, the file script.py needs to be in the working directory.
For more detailed examples, see the commands to launch Python scripts when starting PyMOL. Asynchronous means, that a new Python thread is started:

pymol example.py     # synchronous, in PyMOL module

pymol -r example.py  # synchronous in __main__ module

pymol -l example.py  # asychronous in a new module

You can also launch python programs from within PyMOL with the commands:

run example.py        # synchronous in pymol module

run example.py,main   # synchronous in __main__ module

spawn example.py        # asychronous in a new module

spawn example.py,global # asychronous in the PyMOL module

spawn example.py,main   # asychronous in the __main__ module

Displaying biochemical Properties

• Selecting secondary structures
• Color by atom type from a script
• Displaying double bonds
• Calculating dihedral angles
• Adding hydrogen bonds
• Color by B-factor
• Polar surface area
• Displaying solvent accessible surface
• Display C-Alpha trace of proteins
• Display Phosphate trace of nucleic acids
• Align proteins with CA fit

 

 

Selecting secondary structures

Examples:

select helix, (ss h)

select sheet, (ss s)

select loop, (ss l+'')

 

Color by atom type from a script

The "util" module contains a number of functions that color the atoms according to type, with different colors for the C atoms. For instance,

  util.cbay three

in a .pml script will color object "three" by atom type, with the carbon atoms in yellow ("color by atom yellow").

Other functions from ../modules/pymol/util.py are cbag, cbac, cbas, cbap, cbak, cbaw and cbab (grey (carbon), cyan, salmon, purple, pink, white (hydrogen) and slate).

Lieven Buts

 

Displaying double bonds

You can try going into 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.

Michael George Lerner

 

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

 

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 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
EXAMPLE 2: Show hydrogen bonds between two proteins
There is also a script drawing nice hydrogen bonds fromGareth Stockwell

Warren DeLano

 

Assign color by B-factor

Robert Campbell has a color_b.py python script on hisPyMOL web page that you can use.
it has a number of options including the selection and two types of colouring schemes (rainbow versus a blue-magenta-red gradient) and two types of binning of the colours (equal number of atoms in each colour or equal spacing of colours along the B-factor range).

See http://biophysics.med.jhmi.edu/rlc/work/pymol to download. There is a script 'data2bfacor' to display arbitrary data assigned to atoms as well.

Robert L. Campbell

 

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...

Warren DeLano

 

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

Kaushik Raha

 

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

Warren DeLano

 

Displaying the Phosphate backbone of nucleic acids

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)

Luca Jovine

 

Align proteins with CA fit

If the proteins have significant homology, then 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.

Coloring molecules

• Coloring secondary structures
• Color by atom type from a script
• CMYK-safe Colors
• Color by B-factor
• Creating a Color bar
• Coloring insides and outsides of helices differently
• Coloring all objects differently
• List the color of atoms

   

Coloring secondary structures

Examples:

color red, ss h

color yellow, ss s

color green, ss l+''

When "the colour bleeds from the ends of helices and sheets into loops," try setting cartoon_discrete_colors to 'on' (or 1).

  set cartoon_discrete_colors, 1

or from the the "Cartoon" menu of the external GUI find "Discrete Colors" as the last item in the menu.

Robert Campbell

 

Color by atom type from a script

The "util" module contains a number of functions that color the atoms according to type, with different colors for the C atoms. For instance,

  util.cbay three

in a .pml script will color object "three" by atom type, with the carbon atoms in yellow ("color by atom yellow").

Other functions from ../modules/pymol/util.py are cbag, cbac, cbas, cbap, cbak, cbaw and cbab (grey (carbon), cyan, salmon, purple, pink, white (hydrogen) and slate).

Lieven Buts

 

Use CMYK-safe Colors

Some RGB triplets do have equivalents in CMYK space, and as a result, a figure that looks great on a screen can come out with unpredictable colors when printed.

Most applications do a good job with RGB-to-CMYK conversions for photos, but do not do such a good job with graphics that use pure primary colors. For example, reds are generally OK, but pure blues and greens do not translate very well.

Here are some RGB values that are within the CMYK gamut (i.e. are "CMYK-safe"). In general, colors in PyMOL can be assigned manually:

set_color green= [0.00 , 0.53 , 0.22]

Note that there are default atom colors such as "carbon", "nitrogen", "oxygen", "hydrogen", "sulfur", etc. which should also be redefined:

set_color carbon= [0.00 , 0.53 , 0.22]

Here's still another URL. Although the list of colors is not extensive, you can see colors:CMYK-safe RGB colors

Gil Prive, Dave Fahrney and Warren DeLano

 

Assign color by B-factor

Robert Campbell has a color_b.py python script on hisPyMOL web page that you can use.
it has a number of options including the selection and two types of colouring schemes (rainbow versus a blue-magenta-red gradient) and two types of binning of the colours (equal number of atoms in each colour or equal spacing of colours along the B-factor range).

See http://biophysics.med.jhmi.edu/rlc/work/pymol to download. There are other scripts there as well.

Robert L. Campbell

 

Creating a Color bar

To show a vertical/horizontal color bar indiacting the b-factor variation, use the scriptpseudobar.pml on the structurepseudobar.pdb, or do the following:
1. Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Be sure that CA's are separated by a contant value, say 5 Angstroem.
2. Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).

Bartholomeus Kuettner

 

Coloring insides and outsides of helices differently

Q: does anyone know how to color the inside of helices a different color than the outsides?
A:

set cartoon_highlight_color, red

Warren L. DeLano

 

Coloring all objects differently

Q: Is there a simple way to colour each object currently loaded, with a different colour?

A: There is a script color_obj.py that does the job.
The script is also available at
http://www.ebi.ac.uk/~gareth/misc

USAGE

        color_obj(rainbow=0)

        This function colours each object currently in the PyMOL heirarchy

        with a different colour.  Colours used are either the 22 named

        colours used by PyMOL (in which case the 23rd object, if it exists,

        gets the same colour as the first), or are the colours of the rainbow

Gareth Stockwell

 

List the color of atoms

To retrieve the color for a residue as identified in an expression, you can either iterate over a selection from the PyMOL command line

iterate all, print color

Alternatively, this can be done from a Python script.

Rendering molecules

• Displaying in ball-and-stick mode
• Adjusting width of cartoons
• Calculating a partial surface
• Displaying surface inside a molecule
• Displaying all states of a multiple model/NMR structure
• Displaying dashed lines
• Adjusting size of selection indicators
• Adjusting ray traced picture size
• Ray tracing maps
• Nice PovRay settings
• Making stereo pairs
• Meaning of get_view parameters
• Viewing direction vectors (axes)
• Ray-traceable text labels
• CGO label orientation

 

Displaying in ball-and-stick mode

Q: I've tried several settings and commands but cannot figure out how to make a simple ball-and-stick representation of a molecule. Can it be done in Pymol?

A: Yes, but it is non-obvious:

hide lines

show sticks

show spheres

set stick_radius=0.1

set sphere_scale=0.25

You can change the two numbers above to fit preferences.

Warren DeLano

 

Adjusting width of cartoon

Try varying the following.

For strands:

cartoon_rect_length

cartoon_rect_width

For helices:

cartoon_oval_length

cartoon_oval_width

or for "fancy" helices:

cartoon_dumbell_length

cartoon_dumbell_width

cartoon_dumbell_radius  (radius of cylinder at edge of helix ribbon)

In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.

Robert Campbell

 

Calculating a partial surface

There is a, until now, undocumented way to calculate a surface for only a part of an object without creating a new one:

flag ignore, not A/49-63/, set

delete indicate

show surface

If the surface was already computed, then you'll also need to issue the command:

rebuild

Warren DeLano

 

Displaying surface inside a molecule

As far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source.
The best combination I can find is:

set ambient=0

set direct=0.7

set reflect=0.0

set backface_cull=0

Which gives no shadows and only a few artifacts.
As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray".

util.ray_shadows("heavy")

set two_sided_lighting=1

set backface_cull=0

Warren DeLano

 

Displaying all states of a multiple model/NMR structure

Just go to the movies menue and click 'show all states'.

Jules Jacobsen

 

Displaying dashed lines between two atoms

I think the following commands will do what you want:

        select a, ///A/501/02

        select b, ///B/229/N

        distance d, a, b

This will give you a dashed line object d which is labelled with the distance between the two atoms 'a' and 'b' - you can get rid of the label using

        hide labels, d

btw, if you want to ray-trace the image, I find the dashes come out a bit fat - so I tend to use

        set dash_gap, 0.5

        set dash_radius, 0.1

before the 'ray' command.

Gareth Stockwell

·  Adjusting size of selection indicators

 

Adjusting size of selection indicators

Try:

        set selection_width, 6

        set selection_width, 7

Warren L. DeLano

 

Adjusting ray trace-image size

The pymol ray tracer can generate an image of any size.

ray height,width

Example:

ray 3000,2400

png filename.png

For more options, try 'help ray'

Evan Stein and Ben Cornett

 

Ray tracing maps

For better quality maps with a white background.

set ray_trace_fog,0

set ray_shadows,0

set antialias,1

ray 1600,1200

png img.png

(it will take quite a while...)
Then open img.png using an external image viewer. It should be high enough resolution to print nicely.

Warren DeLano

 

Nive PovRay settings

I typically use the make_pov.py script and "run" it from pymol once to load the function, and then I do "make_pov('povray.inp')" to create the povray.inp file.
Then I edit that file to insert some lines like:

fog {

  distance 10

  fog_type 2

  fog_alt 10.

  fog_offset -160.

  up <0.,1.,.4>

colour rgbt<1.0, 1.0, 1.0, 0.1>

turbulence 0.8

}

In this case I'm not really doing depth-cueing but adding fog at the lower background edge (there were two planes defining the background and a surface below the molecule) rising up towards the front upper edge of the scene.

"fog_type 2" means a "rising fog" along the "up" vector. fog_type 1 is a constant fog. To get pure depth cueing, you would want "up" to be along the <0., 0., 1.> vector (I think!). You'll need to play around with the distance and fog_offset parameters.
You wouldn't necessarily want the "turbulence" parameter in there either.
Check out "Atmospheric Effects" in the povray documentation for many more details:http://www.povray.org/documentation/view/201/

Robert Campbell

 

Making stereo pairs

Try:

ray angle=-3

png image1.png

ray angle=3

png image2.png

This is superior to using the "turn" command because it also rotates the light source. That way shadows will look right.

To make even more beautiful stereo images, use a program like Illustrator or Canvas to add the stereo/depth cued labels. This is a little tricky to describe, but I'll give it my best shot. Place the two images side by side with their centers separated by 6.0 - 6.5 cm, and aligned horizontally. Now add all your labels on the LEFT figure. select all of your labels and duplicate them. Move the duplicated labels to the RIGHT side. For clarity sake let's assume we have 3 labels on the LEFT side (a,b, and c -- we will call then aL and aR for the left and right labels, respectively). Place aL near a recognizable feature of the LEFT figure that you are trying to label. Now horizontilly align aR with aL. Now using only the L/R arrow keys move the aR label until the identical portion of the actual label (let's say the lower right hand tip of the 'a') is vertically aligned with the identical portion of your model (let's say where the C alpha-C beta bond leaves the ribbon backbone) on both the LEFT and RIGHT images. Repeat these steps for each pair of labels. This is a nice method for adding stereo labels because it does not require looking at your computer screen in wall-eyed stereo for 2 hours in order to get proper placement of labels.

By assuring that the labels are positioned in the LEFT and RIGHT images at positions that are identical with respect to the part of the model that is being labeled you automatically are also placing them so they are at the proper depth when the figure is finally viewed in stereo.

Scott Classen and Warren DeLano

 

Meaning of the get_view output

Of the 18 numbers in the output array,
0-8 is the 3x3 rotation matrix,
9-11 is the camera location,
12-14 is the origin of rotation,
15-16 are the clipping distances,
and 17 is the orthoscopic flag.

Robert Campbell, Paolo Martel and Warren

 

Viewing direction vectors

Create a python script (I call it axes.py):

# axes.py

from pymol.cgo import *

from pymol import cmd

from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,

#blue for X, Y and Z

obj = [

   CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,

   CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,

   CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,

   ]

# add labels to axes object (requires pymol version 0.8 or greater, I

# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL

cmd.load_cgo(obj,'axes')

Then you just need to do "run axes.py" from the pymol command line.

You can modify the "3" in the above description of the text labels to change the size of the labels. If you are running a version of pymol older the 0.8, then you cannot add the text (that's why I included colour coding of the axes). You can also use just lines instead of cylinders if you wish:

obj = [

   BEGIN, LINES,

   COLOR, 1.0, 0.0, 0.0,

   VERTEX, 0.0, 0.0, 0.0, VERTEX, 10.0, 0.0, 0.0,

   COLOR, 0.0, 1.0, 0.0,

   VERTEX, 0.0, 0.0, 0.0, VERTEX, 0.0, 10.0, 0.0,

   COLOR, 0.0, 0.0, 1.0,

   VERTEX, 0.0, 0.0, 0.0, VERTEX, 0.0, 0.0, 10.0,

   END,

   ]

would work as well to define the axes object.

 

Ray-traceable labels

You can use the cgo text (line or cylinder versions) as I mentioned in my reply about drawing the xyz axes, but be warned that the labels rotate with your molecule, so getting them oriented perpendicular to the view may be a pain (unless there is something I've missed).

Warren's example from a previous reply of his (cgotext.py):

# draw text using cgo

from pymol import cmd

from pymol.cgo import *

from pymol.vfont import plain

cgo = []

axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]]

pos = [0.0,0.0,0.0]

wire_text(cgo,plain,pos,'Hello World',axes)

pos = [0.0,-3.0,0.0]

cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes)

cmd.set("cgo_line_radius",0.03)

cmd.load_cgo(cgo,'txt')

cmd.zoom("all",2.0)

Robert Campbell

 

CGO label orientation

You could use the cmd.rotate andcmd.translate to position the labels, but it is likely to be somewhat painful. If I'm not mistaken, the rotation will always be about and axis through the origin and so you may need to translate the label into the correct position.

Thus if you have your label in an object called 'text', you could do,

  cmd.rotate(axis='x',angle=20.,object='text')

and repeat this with different angles, until you get the orientation correct. Then use:

  cmd.translate(vector='[1.,2.,3.]',object='text')

(using the appropriate vector, of course!) to position the label.
Not ideal, but if it is sufficiently important, it can be done!

Modeling with PyMOL

• Saving transformed coordinates
• Translate/Rotate objects
• Moving one segment relative to the rest
• Split states to objects
• Altering secondary structures
• Altering van der Waals radii
• Altering atom coordinates
• Deleting bonds
• Converting D- to L- amino acids
• Adding disulfide bonds
• Adding hydrogen bonds
• Protonating ligands
• Superposition of two molecules

 

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).

Paulo Martel

 

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:

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

Warren DeLano

 

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.
EXAMPLE: split.pml

Warren DeLano

 

Split states to objects

There is also a new command in the 0.95 series:

   split_states object-name

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".

Warren DeLano

 

Altering secondary structures:

Examples:

alter A/10:34/, ss='H'

alter A/35:40/, ss='L'

alter A/41:60/, ss='S'

 

Altering van der Waals radii

Example:

alter (elem Fe),vdw=1.8

rebuild

(The value for Fe is wrecked in PyMOL at the moment, so running the above line might be a good idea).

Warren DeLano

 

Altering atom coordinates

Example:

alter_state 1,(pdb1cse),x=x-10.0

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

unbond pk1,pk2

or hit Ctrl-D.

Warren DeLano

 

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.

Warren DeLano

 

Adding disulfide bonds

You can use the "bond" command to attach them:

bond 24/sg,26/sg

bond 56/sg,99/sg

unpick

(unpick will hide the bond baton which gets displayed.)
Additionally, the residue names can be changed for bonded cysteines:

alter cys/,name='CYX'

or for specific residues

alter 24+26+56+99/,name='CYX'

Warren DeLano

 

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 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
EXAMPLE 2: Show hydrogen bonds between two proteins
There is also a script drawing nice hydrogen bonds fromGareth Stockwell

Warren DeLano

 

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...

# 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

Warren DeLano

 

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).

pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and

name P )

Another example:

pair_fit prot1///11-26/CA, prot2///34-49/CA

would superimpose prot1 on prot2 using C-alphas from residues 11-26 in prot1 and 34-49 in prot2.

Movies with PyMOL

• Encoding video files

 

Encoding video files

Assuming you have created a lot of .png files and would like to encode a .mpeg, .avi or other video format, a number of solutions are known:

• The DiVX encoder using mplayer/mencoder? There's binaries for Unix and Windows. It makes rather nice compression on a 800x600 (probably higher). It doesn't take too long to produce the nicer quailty movies, but much longer than simply

·mencoder "mf://*.png" -mf type=png:fps=18 -ovc lavc -o output.avi

·

·Another good program for converting images into movies of different formats isVideoMach : http://gromada.com/VideoMach.html

·

·

·

·TMPGEnc from http://www.tmpgenc.net/ is very fast, easy to use, and produces very nice ouput (MPEG-2). Unfortunately, it does not handle images larger than 720 x 576 pixels.

·

·

·

·The latest Adobe Premiere recipe:

·   Microsoft's MPEG4 V2, 960x720 @ 30 fps, which PowerPoint automatically

·treats as full-screen (due it's wacky metrics).

·

·Using this codec, a recent 24-second movie consumed only 4.5 MB of space,

·but looks much better than a 640x480 Cinepak-based movie with a file size of

·around ~40 MB.  It definitely pays to use the latest technology

·

·

·

·A freeware jiffy to convert png files to an animation isimgcon,

·which proved to be very useful:http://www.fmrib.ox.ac.uk/~yongyue/imgcondl.html

·

·

Advanced PyMOL features

• Meaning of get_view parameters
• Altering atom coordinates
• Translate/Rotate objects
• Moving one segment relative to the rest
• What is in a selection
• How does the density wizard work
• What is molecular sculpting?
• Align proteins with CA fit

 

Meaning of the get_view output

Of the 18 numbers in the output array,
0-8 is the 3x3 rotation matrix,
9-11 is the camera location,
12-14 is the origin of rotation,
15-16 are the clipping distances,
and 17 is the orthoscopic flag.

Robert Campbell, Paolo Martel and Warren

 

Altering atom coordinates

Example:

alter_state 1,(pdb1cse),x=x-10.0

The latter section can contain formulae involving at least the xyz coordinates, lots of constants and the (+-*/) operators.

 

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:

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

Warren DeLano

 

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.
EXAMPLE: split.pml

Warren DeLano

 

What is in a selection?

Atom selections aren't directly exposed to Python, but you can have PyMOL build a Python list containing whatever information you need:

Using PyMOL commands:

list=[]

iterate (name ca),list.append((resi,resn))

print list

[('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), ('LEU',

'6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', '11'),

('CYS', '12'), ('THR', '13')]

or using a Python script (in PyMOL):

from pymol import cmd,stored

stored.list=[]

cmd.iterate("(name ca)","stored.list.append((resi,resn))")

print stored.list

[('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), ('6', '

LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', 'TRP'),

('12', 'CYS'), ('13', 'THR')]

Warren DeLano

 

How does the Density Wizard work?

The answer:

·  Load a map

·  Load a model structure

·  Activate the Density Wizard

·  Control-middle click to pick any atom in the model to get the map drawn about it. Each of the blue rows in the Wizard is a pop-up menu. You can select multiple or different maps to be displayed at different levels as you traverse the model.

Warren DeLano

 

What the heck is molecular sculpting?

Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL.

To actually use this feature:

1. Load a PDB file.
2. Configure the mouse for editing (Mouse menu) or click in the mouse/key matrix box.
3. Select "auto-sculpting" from the Sculpting menu.
4. Select Sculpting from the Wizard menu.
5. Ctrl-middle-click on any atom in your protein to activate sculpting
   the green part will be free to move
   the cyan part will be a fixed cushion to provide context
   the grey part will be excluded.
6. Now perform any conformational editing operation in the green region such as:
   ctrl-left-click-and-drag on an atom
   ctrl-right-click on a bond, then ctrl-left-click-and-drag about that bond.

You can adjust the radius and cushion using the blue pop-up menus.

Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future.

Warren DeLano

 

Align proteins with CA fit

If the proteins have significant homology, then 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.

Python scripting

• Launching Python programs
• Using the PyMOL commandline
• What is in a selection
• Does a selection exist
• Get Coordinates from python
• Create objects from PDB strings
• Measure distances from python
• Coloring all objects differently
• List the color of atoms
• List secondary structures
• Process key events from shell
• Alter key bindings
• Viewing direction vectors (axes)
• Ray-traceable text labels
• CGO label orientation
• 3D marks on atoms
• Save and load objects (pickle)
• Building ChemPy models

   

Launching Python programs

1. Running a Python script from PyMOL, usually the command:

run script.py

Is enough. Of course, the file script.py needs to be in the working directory.
You can also launch Python scripts when starting PyMOL. Asynchronous means, that a new Python thread is started:

pymol example.py     # synchronous, in PyMOL module

pymol -r example.py  # synchronous in __main__ module

pymol -l example.py  # asychronous in a new module

You can also launch python programs from within PyMOL with the commands:

run example.py        # synchronous in pymol module

run example.py,main   # synchronous in __main__ module

spawn example.py        # asychronous in a new module

spawn example.py,global # asychronous in the PyMOL module

spawn example.py,main   # asychronous in the __main__ module

2. Running PyMOL from a Python script requires two commands:

import pymol

pymol.finish_launching()

 

Using the PyMOL commandline

Are you aware that the PyMOL command line is also a Python command line? You can just use PyMOL interactively in that fashion.

PyMOL>print 1+1

2

PyMOL>from random import random

PyMOL>print random()

0.739460642143

The only major difference is that the default namespace for PyMOL is "pymol" not "__main__"

PyMOL>print __name__

pymol

Warren DeLano

 

What is in a selection?

Atom selections aren't directly exposed to Python, but you can have PyMOL build a Python list containing whatever information you need:

Using PyMOL commands:

list=[]

iterate (name ca),list.append((resi,resn))

print list

[('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), ('LEU',

'6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', '11'),

('CYS', '12'), ('THR', '13')]

or using a Python script (in PyMOL):

from pymol import cmd,stored

stored.list=[]

cmd.iterate("(name ca)","stored.list.append((resi,resn))")

print stored.list

[('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), ('6', '

LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', 'TRP'),

('12', 'CYS'), ('13', 'THR')]

Warren DeLano

 

Does a selection exist?

The function below will return true if the selection is defined.

from pymol import cmd

from types import *

def sele_exists(sele):

    sess = cmd.get_session()

    for i in sess["names"]:

        if type(i) is ListType:

            if sele==i[0]:

                return 1

    return 0

Igor Pechersky

 

Get coordinates from Python

The actual C-langauge arrays aren't exposed, but there are at least three different ways you can modify coordinates from within Python:

·  You can get a python object which contains the molecular information, modify the coordinates in that object, load the modified molecule into PyMOL, update the modified coordinates to the original model, and then delete the modified object. (Example in a python script)

·  Another approach is the "alter_state" function, which can perform the same transformation in a single PyMOL command statement:

alter_state 1,pept,(x,y)=(-y,x)

Likewise sub-selections can be transformed as well:

alter_state 1,(pept and name ca),(x,y,z)=(x+5,y,z)

·  A third approach is to use alter_state with the global "stored" object:Example in a Python script) Approaches 2 gives the best performance, approach 3 gives more flexibility, and approach 1 gives you a reusable and fully modifiable Python object.

Warren DeLano

 

Create objects from PDB strings

I thought I'd post this example, just in case anyone else cares about this:

delete all

cmd.read_pdbstr("""HEADER    CREATED BY CONVERTPROSPECT              27-JAN-02   2tnf  \

REMARK   1                                                                       \

ATOM      1  N   PRO A   9       1.895  67.213 -38.182  1.00  0.00           N   \

ATOM      2  CA  PRO A   9       1.703  68.680 -38.402  1.00  0.00           C   \

....

ATOM   1153  C   GLY A 157       6.927  59.108 -38.901  1.00  6.00           C   \

ATOM   1154  O   GLY A 157       6.700  59.292 -37.676  1.00  6.00           O   \

TER    1155      GLY A 157                                                       \

MASTER                                                                           \

END                                                                              \

""","2tnfa")

hide all

show cartoon

color grey

....

Reece Hart

 

Measure distances from Python

Use Python (and the run command with .py files).

from pymol import cmd

f=open('dist.txt','w')

dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha')

f.write("%8.3f\n"%dst)

f.close()

You could measure the whole protein this way by putting a loop around the distance command:

from pymol import cmd

f=open('dist.txt','w')

atom = cmd.get_model("mol1////ha").atom

for i in range(len(atom)-1):

   sele1 = 'mol1///%s/HA'%atom[i].resi

   sele2 = 'mol1///%s/HA'%atom[i+1].resi

   dst=cmd.distance('tmp',sele1,sele2)

   f.write("%14s %14s %8.3f\n"%(sele1,sele2,dst))

f.close()

The output "dist.txt" would then look like:

   mol1///4/HA    mol1///5/HA    4.748

   mol1///5/HA    mol1///6/HA    4.828

   mol1///6/HA    mol1///7/HA    4.861

   mol1///7/HA    mol1///8/HA    4.784

   mol1///8/HA    mol1///9/HA    4.936

   mol1///9/HA   mol1///10/HA    4.833

  mol1///10/HA   mol1///11/HA    4.933

  mol1///11/HA   mol1///12/HA    4.813

Warren DeLano

 

Coloring all objects differently

Q: Is there a simple way to colour each object currently loaded, with a different colour (in the same way that you can colour each chain in a molecule differently)? This would be really useful in visualising a set of superposed structures.

A: There is a script color_obj.py that does the job.
The script is also available at
http://www.ebi.ac.uk/~gareth/misc

USAGE

        color_obj(rainbow=0)

        This function colours each object currently in the PyMOL heirarchy

        with a different colour.  Colours used are either the 22 named

        colours used by PyMOL (in which case the 23rd object, if it exists,

        gets the same colour as the first), or are the colours of the rainbow

Gareth Stockwell

 

List the color of atoms

To retrieve the color for a residue as identified in an expression, you can either iterate over a selection from the PyMOL command line

iterate all, print color

Alternatively, this can be done from aPython script.

import pymol

pymol.color_list = []

cmd.iterate('all', 'pymol.color_list.append(color)')

print pymol.color_list

Warren DeLano

 

List secondary structures

Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS') with the following script:

import pymol

pymol.stored_ss = []

cmd.iterate('all', 'pymol.stored_ss.append(string.ljust(ss,1))')

print string.join(pymol.stored_ss)

Warren DeLano

 

Process key events from shell

The following scripts turns the view 30 deg around the y-axis, each time you press the enter key in the python shell (the original shell you started pymol from), just as an example:

#use "spawn spawn_demo.py, local" to invoke this python script from

within pymol

wait=""

i=0

while i < 12 and wait!="x":

  cmd.turn("y", 30)

  print "Press enter key to continue or x + enter to terminate"

  wait=raw_input()

  i=i+1

print "Done"

Markus Meier

 

Alter key bindings

It's not GUI, but you could simply bind a function key such as F1 to a command:

cmd.set_key('F1',lambda :cmd.show('sticks'))

Warren DeLano

 

Viewing direction vectors

Create a python script (I call it axes.py):

# axes.py

from pymol.cgo import *

from pymol import cmd

from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,

#blue for X, Y and Z

obj = [

   CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,

   CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,

   CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,

   ]

# add labels to axes object (requires pymol version 0.8 or greater, I

# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL

cmd.load_cgo(obj,'axes')

Then you just need to do "run axes.py" from the pymol command line.

You can modify the "3" in the above description of the text labels to change the size of the labels. If you are running a version of pymol older the 0.8, then you cannot add the text (that's why I included colour coding of the axes). You can also use just lines instead of cylinders if you wish:

obj = [

   BEGIN, LINES,

   COLOR, 1.0, 0.0, 0.0,

   VERTEX, 0.0, 0.0, 0.0, VERTEX, 10.0, 0.0, 0.0,

   COLOR, 0.0, 1.0, 0.0,

   VERTEX, 0.0, 0.0, 0.0, VERTEX, 0.0, 10.0, 0.0,

   COLOR, 0.0, 0.0, 1.0,

   VERTEX, 0.0, 0.0, 0.0, VERTEX, 0.0, 0.0, 10.0,

   END,

   ]

would work as well to define the axes object.

 

Ray-traceable labels

You can use the cgo text (line or cylinder versions) as I mentioned in my reply about drawing the xyz axes, but be warned that the labels rotate with your molecule, so getting them oriented perpendicular to the view may be a pain (unless there is something I've missed).

Warren's example from a previous reply of his (cgotext.py):

# draw text using cgo

from pymol import cmd

from pymol.cgo import *

from pymol.vfont import plain

cgo = []

axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]]

pos = [0.0,0.0,0.0]

wire_text(cgo,plain,pos,'Hello World',axes)

pos = [0.0,-3.0,0.0]

cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes)

cmd.set("cgo_line_radius",0.03)

cmd.load_cgo(cgo,'txt')

cmd.zoom("all",2.0)

Robert Campbell

 

CGO label orientation

You could use the cmd.rotate andcmd.translate to position the labels, but it is likely to be somewhat painful. If I'm not mistaken, the rotation will always be about and axis through the origin and so you may need to translate the label into the correct position.

Thus if you have your label in an object called 'text', you could do,

  cmd.rotate(axis='x',angle=20.,object='text')

and repeat this with different angles, until you get the orientation correct. Then use:

  cmd.translate(vector='[1.,2.,3.]',object='text')

(using the appropriate vector, of course!) to position the label.
Not ideal, but if it is sufficiently important, it can be done!

Robert Campbell

 

3D marks on atoms

Here's a script graph.py which can be used to put marks on the positions of every atom in a selection. There are several types of marks included now, e.g. cube, rhombic dodecahedron, tetrahedron, plus and star. Using a matrix operator these can be extended a bit, to 2D counterparts for example, or to elongated or rotated shapes. I should still include some documentation but in brief the usage is as follows:

graph selection = '(all)', shape = 'plus' | 'sphere' | 'star' | 'tetrahedron' | 'dodecahedron', size = 1, r = 0.10, rgb1 = [1,0,0], rgb2 = [0,0,1], mtx = [[1,0,0],[0,1,0],[0,0,1]], name = "graph"

Selection should be obvious, as is shape. Size is a relative indicator for the size, though at present I haven't fixed things such that a size 1 tetrahedron matches a size 1 dodecahedron. r is the radius of the lines. rgb1 and rgb2 are the start and end color for each line. mtx is the matrix operator, which works on the original shape centered around the origin (before translation to the point of the atom from the selection).

Tserk Wassenaar

 

Save and load objects

There is a convenient format: ".pkl", that works like PDB, but is a Pickled copy of the PyMOL Model Class. The main advantage this has over .pdb is that it saves and restores extra properties such as secondary structure code, atom types, van der waals radii, formal and partial charges, etc.

load myprot.pdb

dss

show cartoon

alter 100-110/, ss='H'

alter 65-67,ss='L'

save myprot.pkl

... quit program, complete your PhD, take a vacation, and come back...

load myprot.pkl

show cartoon

will work.

".pkl" has the additional advantage of being a simple molecular object useful in straight Python, outside of PyMOL. All you need to do is have a copy of PyMOL's "chempy" module available in your PYTHONPATH

from chempy import io

model = io.pkl.fromFile("myprot.pkl")

for atom in model.atom:

   print atom.name

Warren DeLano

 

Building ChemPy models

This is a snap. Just "run" the following Python program from within PyMOL.

from chempy.models import Indexed

from chempy import Bond, Atom

from whrandom import random

from pymol import cmd

model = Indexed()

# create some atoms

for a in range(1,11):

   at = Atom()

   at.name = "X%02d"%a

   at.coord = [random()*5,random()*5,random()*5]

   model.atom.append(at)

# now create some bonds

for a in range(1,10):

   bd = Bond()

   bd.index = [a-1,a] # zero-based indices!

   model.bond.append(bd)

# now load and label

cmd.load_model(model,"example")

cmd.label("example","name")

本文引用地址：http://blog.sciencenet.cn/blog-355217-279196.html