PyMOL Manual 1.0

Joshua D Brown

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Table of Contents

Interface……………………………………………………….3 Mouse Controls……………………………………….…….5 Visible Slab……………………………………………………8 Selecting……………………………………………………...10 Commands…………………………………………………..11 Enabling/Disabling………………………………………13 Show/Hide…………………………………………………..14 View……………………………………………………………15 Drag…………………………………………………………….16 Builder………………………………………………………...17 Chemical Display……...………………………………….18 Protein Display…………………..……………………….20 Sculpting……………………………………………………..23

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Interface

Viewer o Displays all 3D graphics and location of direct user interaction

with 3D model o Also contains a command line

Internal GUI o Contains list of “Objects” load, mouse button configuration matrix,

and movie controls External GUI

o Contains Command Input Field

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Interface with Labeled controls

Command Line – area where the user can enter commands which PyMOL will carry out Names Panel – Lists all of the objects and selection-names currently loaded in PyMOL Mouse Matrix – Shows all commands for Mouse Controls and shows what mode the mouse is currently in

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Movement and View Manipulation

There are two modes for Mouse Control: Viewing and Editing. To toggle between these two modes, click on the Mouse Matrix Controls in the bottom of the

Internal GUI. Make sure when operating PyMOL that you are in the correct Mouse Mode.

Mouse Controls Viewing Mode

Keyboard Modifier

Left Click Middle Click Right Click Wheel Scroll

None Rotate Camera Move Camera

XY Plane

Move Camera Z

Plane (Zoom)

Adjust width of visible slab

Shift Key Select Box Deselect Box Move

Clipping Planes

Move visible Slab

Control Key Select

Pick multiple atoms (can

select up to 4)

Pick one atom (can select only

one at a time)

Zoom in

Control + Shift Key

Select (one selection

at a time)

Set origin of rotation

Move Clipping Planes

Move Camera Z Plane (Zoom)

Single Click Select

Center view on

atom Menu -

Double Click Menu -

Pick multiple

atoms (can select up to

4)

-

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Mouse Controls Editing Mode

Keyboard Modifier

Left Click Middle Click Right Click Wheel Scroll

None Rotate Camera Move Camera

XY Plane

Move Camera Z

Plane (Zoom)

Adjust width of visible slab

Shift Key Rotate Object Move Object

XY Plane

Move Object in Z

Plane

Move visible Slab

Control Key Move an atom

Select

Select a bond for Rotation

Zoom in

Control + Shift Key

Move an atom in the Z plane

Set origin of rotation

Move Clipping Planes

Move Camera Z Plane (Zoom)

Single Click Pick multiple

atoms (can select up to 4)

Center view on atom

Menu -

Double Click Move an atom Activate

Dragging-

Select a bond for Rotation

-

To Practice open a pdb file. This can be done by typing in the Command Input Field: Syntax fetch file_name Example fetch 2jpr A PyMOL file containing the N-terminal domain of the HIV capsid protein should open.

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Mouse Control Descriptions

Rotate Camera

The rotation control works as if there is an invisible ball at the origin of rotation. If you click on the ball and drag, it is as if you put your finger on the sphere and rotate it in the same manner If you click outside the sphere the rotation will only be about the Z-axis. So, if you want to rotate the view “clockwise” or “counter-clockwise” than click near the edges of the screen and adjust. Use practice to become familiar where the edges of the “invisible” track ball are.

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Visible Slab PyMOL is a three dimensional program and the Visible Slab is a feature that makes only a certain layer visible, so that the user may focus on the internal aspects of the model. Example: Here is a long chain molecule viewed from the side and the front.

Looking from the front view the whole molecule is visible, therefore the Visible Slab encompasses the whole molecule. The Visible Slab can be adjusted so that only a “slice” of the molecule is visible.

Here is the same molecule with a thinner Visible Slab. The Bottom picture shows the same molecule and shows the location of the Visible Slab from the side view. Everything outside of the Visible Slab is invisible.

Side View

Front View

Location of Visible Slab

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Visible Slab Manipulation Wheel scroll + No Keyboard Modifier – adjusts the width of the visible slab Example: Scrolling Up increases the width

Scrolling Down decreases the width

Wheel scroll + Shift – moves the Visible Slab

Location of Visible Slab

Location of Visible Slab

Location of Visible Slab

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Selecting The selecting features allows objects to be selected for further manipulation At the bottom of the Internal GUI is the option to what type of objects are selected.

The options are: Segments, Objects, Molecules, C-alphas, Atoms, Residues, Chains Left Click + Shift – Select Box Middle Click + Shift – Deselect Box This simply creates a box and all objects within the box will be selected and vice versa for the Deselect Box; everything within the Deselect Box will be deselected.

Picking Atoms This feature is to select atoms within the molecular graph. This is for manipulation on a different level than just ordinary selecting. When selecting atoms within the molecular graph the distances, Hydrogen bonds, and other characteristics can be displayed.

This picture shows two atoms (pk1 and pk2) selected with the distance between the two atoms displayed in Angstroms. A maximum amount of 4 atoms can be selected. They are termed pk1 through pk4 The amount of ribbons depicts its label.

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Commands PyMOL commands can be typed into the bottom of the Viewer screen or in the External GUI. Cut, Copy, and Paste cannot be used in the Viewer Command bar, but can be used in the External GUI. You must use hotkeys (Control+V, Control+C, Control+X) Syntax – the form and grammar of the command code. Make sure to pay attention to commas and spaces All typed commands will be recorded in the log history in the External GUI. Press “esc” to view the log command in the Viewer

Loading/Fetch Loading – you are able to load a pdb file that is saved on your computer by typing:

Syntax load directory Example load username/desktop/PyMol/practice.pdb This goes to the directory and opens the designated file

Fetch – this is similar to loading, but instead of the desired file being retrieved from your computer it is retrieved from the online Protein Data Bank.

Syntax fetch pdb code Example fetch 2jpr Retrieves pdb file from online data bank

Saving To save simply type the command. Make sure to type .pdb at the end. Syntax save namedirectory Example save practicename.pdb This will save the PyMOL file in pdb format. It should be located under the user folder

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Load a practice model: Syntax fetch file_name Example fetch 2jpr Retrieves pdb file from online data bank

Selection-Expression Selection-Expression are ways to describe specific items within PyMOL for example atoms, residues, molecules, helices, etc. Example: resi 4 This selection-expression represents residues 4 resi 4+9 This selection-expression represents residues 4 and 9 resi 1-32 This selection-expression represents residues 1 through 32 A complete list of Selection-Expressions will be provided

Selection-Name When you select specific molecules in PyMOL, you are able to label the selection for easy use and reselection. This is called a Selection-Name. The selection-name can be anything within upper and lower case letters, numbers (0 to 9), and the underscore character. Avoid anything else. The selection-name is case sensitive. The use of selection-names will be explained later on. Note: When a command does not contain a selection-name or expression, the default is all objects loaded in PyMOL When an item is selected (highlighted by pink dots) it is automatically defaulted the Selection-Name “sele” while it is selected.

Syntax select selection-name, selection-expression Example select pocket, resi 5-9 Assigns a selection-name is residues 5 through 9

Object-Name Object-Names are different from Selection-Names. Object-Names are created when PyMOL locates data from a loaded data file. Selection-Names are more of a superficial label, while Object-Names are more concrete. When a Selection-Name is deleted the data is still under the Object-Name When an Object-Name is deleted, the data must reload again.

General Overview

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Selection-Expression – preprogrammed ways to describe items/atoms/molecules in PyMOL Selection-Name – label the user is able to assign to a their choice of items Object-Name – a more concrete name to the loaded molecules. In the top of the Internal GUI is a list of all the current Selection-Names and Object-Names. Selection-Names are in parenthesis to distinguish from Object-Names

Enabling and Disabling Objects and Selections Objects: Enabling and Disabling Objects will affect the objects representation (it will appear or disappear) Syntax enable object-name Example enable 2jpr The Object, 2jpr, will be enabled (appear) Syntax disable object-name Example disable 2jpr The Object, 2jpr, will be disabled (disappear) Selections: Enabling and Disabling Selections will only select or deselect the items (the pink dots will appear or disappear) Syntax enable selection-name Example

enable pocket the selection-name, pocket, will be selected (pink dots will appear)

Syntax disable selection-name Example

disable pocket The selection-name, pocket, will be deselected (pink dots will disappear)

Mouse Control Alternative: You are also able to click on the object-name/selection-name in the control panel at the top of the Internal GUI to trigger the items enabled or disabled.

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Show/Hide Representations The model/atoms can be shown in a variety of representation. The choices are: lines, spheres, mesh, ribbon, cartoon, sticks, dots, and surface. To change the representation type:

Syntax show representation Example

show sticks The object is represented as sticks When you choose to show an object in a certain representation, the last representation will still be present, so you must get rid of the first one Syntax hide representation Example

hide lines The lines representation disappears. You will not be able to see this because the stick representation overlaps the lines.

Color Syntax color color-name, selection-expression or selection-name Example

color brown, pocket the residues previously labeled under the selection-name, pocket, are changed to the color brown.

color brown If no selection-name or selection-expression is provided then by default all atoms loaded in PyMOL will be colored brown

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Changing View Along with mouse controls, commands can be used to change the point of view

Zoom Zoom brings an object or selection close up to the center of the field of view or zooms out to include it.

Syntax

zoom selection-expression Example

zoom pocket The view will change to zoom in/out on pocket

Orient This is similar to zoom, but PyMOL will change the angle to align the object or selection so its largest dimension is shown horizontally and its second largest dimension is shown vertically.

Syntax

orient selection-expression Example

orient pocket The view is changed for maximum visibility of the selection

View PyMOL is also able to save views for recall later. This only saves the viewpoint not the representation. You must also give the saved view a “key” or name.

Syntax

view key, action The two actions are store or recall Example

view frontpocket, store The current view is labeled “frontpocket” and stored. view frontpocket, recall The stored view, “frontpocket,” is recalled view frontpocket recall is the default option so this will also recall the stored view, “frontpocket.”

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Drag Drag is the feature to move objects or molecules in PyMOL First you must activate drag on the desired object Syntax

drag selection-name Example

drag pocket The item named under “pocket” is not activated for dragging.

A menu will appear at the bottom of the Internal GUI for dragging. It contains options for undo, redo and indicate. Undo and redo only affect object movements. Indicate simply selects the object that is activated for dragging

Dragging Controls Keyboard Modifier

Left Click Middle Click Right Click

Shift Rotate Object Move Object

XY Plane

Move Object in Z

Plane Note: Shift must be held down When dragging is complete you may hit done in the Dragging Menu at the bottom of the Internal GUI or left click on empty space or another object.

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Builder PyMOL contains a Builder feature in which the user can build molecules. To open this Builder feature you must rename MacPyMOL 2 to PyMOLX11Hybrid.

When you open PyMOL this way it will change the External GUI to a more user friendly version for the Builder feature. The External GUI will also be in a separate window.

This is what the External GUI should look like Click on the Builder Button and the Builder Menu should open

Builder Menu The Builder Menu comes with many options to choose from. There are two main displays: Chemical and Protein

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Chemical Display

The chemical display is for building molecules of your choice from scratch. It has a few options of pre-built molecules that you can start from such as the cyclic compounds and commonly found bonds shown. To begin, click on the option where you would like to start. Example: Click on “CH4” No molecule will show up yet. In the top left corner of the Viewer it will give you the option to pick the location to attach the methyl.

You can attach the methyl to an existing object If you starting from scratch you must click on “Create As New Object” in the bottom of the Internal GUI

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To add additional methyl groups: Mouse Mode Viewing – Control + Middle click on the Hydrogen Atom Mouse Mode Editing – Left Click on the Hydrogen Atom You can continue this to make the hydrocarbon chain as long as you wish. You can also switch to a different functional group and repeat the same process. Elements: You can click on one of the elements in the top row and you are able to replace any atom in the molecule with that element. Make sure to click on the actual atom you wish to substitute, not where you want the new element to be attached to.

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Protein Display

This menu is useful for building long chain of amino acid so that you do not have to produce them from scratch

You click on the first amino of choice and click “Create As New Object.” An atom on the newly create amino acid will be selected. This is just to show where the next amino acid will be attached to. You can continue to click on the next amino acid of your choice and PyMOL will continue to add the amino acids to the chain.

Other Options

There is another menu below the Chemical/Protein Display. It has a variety of options to modify the molecules being built Charge [+1, 0, -1] You may assign a formal charge to any atom in the molecule. Simply click on the desired charge and than select the atom Mouse Mode Viewing – Control + Middle click on the atom Mouse Mode Editing – Left Click on the atom

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Bonds The sub-options under Bonds are to the right of it. Create, Delete, Cycle, I, II, III, Arom Create This option is to create a bond. When it is clicked it will give you the option to click on two atoms and it will than create a bond between those atoms. This option is useful for making cyclic compounds. Mouse Mode Viewing – Control + Middle click on the atom Mouse Mode Editing – Left Click on the atom Delete This option is simply to delete bonds. Click on delete and than on the bond you wish to delete Cycle, I, II, III, Arom This option allows you to change the characteristics of a bond. You make it single, double, or triple. The cycle options simply toggles through all of the choices, including Aromatic. Fix H - Used to fix Hydrogens in their position Add H - Used to add Hydrogens to an atom Delete – Deletes atoms. It will also delete any hydrogens attached to that atom. Clear – deletes everything load in PyMOL. Invert - Used to change to the stereochemistry of a chiral center. After activating this feature you must select three atoms 1st Atom – Origin atom for Inversion (Chiral Center) 2nd Atom – First stationary atom 3rd Atom – 2nd Stationary Atom For the 2nd and 3rd atom you basically pick the two atoms attached to the 1st atom (origin/chiral atom) that will not invert. There will only be two atoms that are not selected and these two atoms will switch places Example: If we wanted to invert the orientation of this molecule by switching the position of the light blue and purple atom, the 3rd atom we would select would be the red atom.

Origin Atom

2nd Atom

3rd Atom

After Inversion

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Clean – clean changes the conformation of the molecule so that torsional strain and Van der Waals forces are minimized. This feature should be used when you done building your molecule or amino acid sequence.

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Sculpting Sculpting is a feature in PyMOL in which is induces changes in the conformation of molecules due to spatial volume, torsional strain and Van der Waal’s forces. It does not take into consideration energy minimization or thermodynamics. To activated go to the top Menu Bar > Wizard > Sculpting Once activated a Sculpting Menu will appear in the bottom of the Internal GUI and in the top left corner of the Viewer it will ask you to pick a center atom. The Center atom is the center of the sculpting

Residue Shells: option on what is to be sculpted. It can be toggled to One Residue. Residue Shells means multiple residues within proximity of the center atom will be sculpted. Radius: area of affected sculpting Cushion: fixed area around sculpting area

Toggle Sculpting: to deactivate or activated sculpting Toggle Bumps: to show or hide Van der Waal’s bumps Relocate: to relocate center atom Once you left click on an atom to designate it as the center atom, sculpting will begin based on the settings chosen. Click done to end sculpting.

The green colored molecules are is the area that is being sculpted The blue colored area are the fixed molecules The gray molecules are not apart of the sculpting process The green dots represent the Van der Waal’s forces. They can be in red when the forces are large

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Movie Step by step for sculpting List of commands Distance Notes:

Selection-Expressions o ss h – helices o ss s – beta sheets o ss 1+ - loop and unassigned residues o distance

mode=2 o count_atoms