Pymol tips and tricks Gates, Kent S. Univ of Missouri
Appendix 1: Pymol Commands • Downloading Pymol To download Pymol, go to www.pymol.org or Google ‘Pymol’. The program is called Pymol. Go to "products" tab. Then the "Pymol" link. Then look for "educational subscriptions" link or go directly via http://www.pymol.org/educational . Then look for the words "register for educational-use-only pymol" and the associated "register here" link. Fill out an agreement that specifies academic use, then you get a code that allows FREE downloading of the program. • Downloading a pdb file Go to www.rcsb.org or Google ‘pdb’. At the pdb website, type into the search bar at the top your assigned coordinates of “for example, 1C83”.
On the left side of the page are several drop-down menus. The second from the top is “Download Files”. Click on this and it will drop down some options. Click on “PDB text” and save the file where you can easily find it. • Opening a pdb file In Pymol, open a file by clicking File -> Open… Locate and click on the pdb file you downloaded from the web. You should see the structure in the viewer of Pymol. • Using the mouse To get the most out of Pymol, a three-button mouse is required. The scroll wheel can be used as a button by clicking and holding. Try out the mouse commands as detailed below on your newly loaded protein structure.
On a single button laptop (Mac), you can rotate the protein simply by holding down the button and sliding your finger on the track-pad. You can center the protein in the window using option-click and you can zoom using control-click. You change the size of the “slice” that you are viewing with control-shift-click.
Pymol tips and tricks Gates, Kent S. Univ of Missouri
Std Commands:
“reset” (double click on image window, “reset” on menu, centers protein in window) select all, then type: “center” (centers structure in window) hide all show cartoon show side chain, resi 215 Setting→Cartoon→Side Chain Helper color gray90 color atom (gives color by atom identity) show spheres, resi 301 color white, resi 301 color gold, resi 200-221 hide everything, resi 301 zoom: option, click, slide on trackpad move x/y on page: control, click, slide on trackpad
Rendering and Saving: Click on the “Ray” button (in the top right corner of the Pymol interface). It will take a few seconds to render. To save the snapshot (select: File → Save Image)
Rock: Click “rock” button in the upper right corner of the user interface.
Appendix 2. Pymol “Tricks”
• Zoom resi X-X or zoom resi X (zooms to a section of the protein)
• Orient (resets the view to “normal”)
• Center the image: center
• If the center of rotation seems "off" try these things: middle click on the desired rotation center. You can also pull down the action menu of one of the ligands or crossclusters and click "center". JJT.
• Under the menu: Settings → Cartoon → Fancy Helices you can get cool looking tubular edges to the helices. A nice touch.
• Altering the properties of individual atoms in the structure: Control click… a menu appears on top of the atom. In this menu, under heading of “atom” you can color, show, label, etc.
• Measuring distances in the structure. Under the Wizard menu, select “measurement”. Then click sequentially on the two atoms of interest. A yellow “ruler” appears between them. This function stays on until you click “done” in the
Pymol tips and tricks Gates, Kent S. Univ of Missouri measure window on the right side of the GUI. You can hide the distance label by PyMOL>hide labels
• Selecting a set of residues: select aas, resn cys
• or select aas, resn cys + phe
• or, in a DNA duplex select aas, resn a + g
•• To name a selection, for example: set_name sele, Alanines
• Selecting all carbons: sele symbol c
(coloring carbons gray helps me because I can’t see yellow sulfurs against the green default color that Pymol uses for carbons)
• Select all Gly: sele resn gly
• Selecting a set of residues: sele resi 1-10
• or: sele resi 1+5+7
• Selecting all α and β carbons: sele name ca+cb
• Selecting helices, sheets, loops: sele ss h OR sele ss s OR sele ss “”
• One could also color helices, sheets, and loops, e.g.: color purple, ss h
• Hide solvent: hide (solvent)
• Change background color to white: bg_color white
• Electrostatic potential surface: On the right menu of objects and selections (the GUI), for example: under the “A” heading for 1C83_PTP1B_ligan, go to “generate” then “vacuum electrostatics” then “protein contact potential (local)”.
• Add hydrogens to protein: h_add 1C83
• You can make a surface view partially transparent (0-1) so that you can see the cartoon beneath: show surface THEN type: set tranparency=0.5 (0.1 is less transparent and 0.9 is more transparent).
• Spheres can also be made transparent (0-1): set sphere_transparency=0.7
• Size of spheres can also be changed (0-1): set sphere_scale=0.5 (I’m not sure what the default size is… just have to play around with this)
• The extent of depth-cued fog (0-1) is controlled by: set fog=0.5 (In my experience this effect is only striking when the background is white. Again, I’m not sure what the default setting is – zero is less foggy, one is more foggy).
Pymol tips and tricks Gates, Kent S. Univ of Missouri
• The use of antialias reportedly greatly affects the quality of the image after ray- tracing (and the also the time that rendering will require). Antialias is either “on” or “off”. Set antialias=0 or 1 (before clicking “ray”).
• Structural alignment of two homologous proteins: In this example, you are going to align PH acylphosphatase (1w2i) and bovine acylphosphatase (2ACY). File -> Open -> 1w2i_nowat.pdb File -> Open -> 2ACY.pdb
Pymol> align 1w2i_nowat, 2ACY you should see the following in the text window: ExecutiveAlign: 446 atoms aligned ExecutiveRMS: 23 atoms rejected during cycle 1 (RMS=0.86) ExecutiveRMS: 20 atoms rejected during cycle 2 (RMS=0.63) Executive RMS = 0.541 (403 to 403 atoms) In this case, the RMSD is 0.541 Å More often, people report Ca RMSD values which can be determined by: Pymol>align 1w2i_nowat and name ca, 2ACY and name ca
• How to handle structures that are dimeric, trimeric, etc. Each subunit usually has a chain identifier a, b, c… Often it might be desirable to view just one subunit Type: - hide everything, all - show cartoon, chain a or - show cartoon, chain a - hide everything, not chain a or -hide everything, all -show cartoon, chain a show sticks, chain a and resi 213-216 if, during manipulation of the protein, things on the “invisible” subunits show up, just type “hide everything, not chain a” again.
((Alternatively, it might be preferable to open the .pdb file using a program like TextEdit on the Mac. Then, simply delete the coordinates for one or more of the monomers)).
Or…..
• How about when there are two proteins shown in the unit cell, but I only want to look at one (and get rid of the other)? – under “display” menu select “sequence on”. A bar will appear above the structure showing the amino acid sequence of all protein chains in the window. Use option-shift to select all aa for one chain. Then on the right for the (sele) go to the A (actions) menu and select “remove atoms”. Second protein… gone!
Pymol tips and tricks Gates, Kent S. Univ of Missouri
• Pymol has no ball-and-stick mode; however, it can be simulated with a combination of spheres and sticks.
>show spheres
>show sticks
>set sphere_scale, 0.3 (0.15, for small little knobs)
>set stick_radius, 0.2
sticks and balls will be the same color. If different colors are desired, this can be achieved by creating separate objects for each.
• How do I crank-up the glossiness of rendered atoms? Type–> set spec_power = 200 (# in range 20 – 250) And–> set spec_refl=1.5 (# in range 1.0 - 2.0) Note that the shadow options in the Display menu of the external GUI may modify these parameters.
• Explore the “Actions” menu. For example: Locate the molecule name you loaded in the right hand menu bar, On the same line as your molecule, click on A (Actions) -> preset -> pretty
• Showing entire structure when only “half” of the structure is shown due to symmetry. (Often in DNA structures). -click on A (actions) -> generate -> symmetry mates -> within 5 A. Then go to the all heading and “hide all”… then one-by-one show the selections until you find the pair in which you are interested.
• Generating “symmetry pairs” in a structure (longer explaination of the topic above). Many DNA structures will show only one strand of the duplex because the structure is symmetrical.
View the molecule in cartoon format. Pymol can use the symmetry information (indicated in the text file you downloaded) to generate the symmetry related molecules. - Click on A (actions) -> generate -> symmetry mates -> within 5 Å
Zoom out a bit and you will see that Pymol generated quite a number of neighboring molecules that are all present in the crystal and related by crystallographic symmetry. I have colored the original molecule differently from the rest using the color boxes on the right side of the molecule menu. You can make the same change to all
Pymol tips and tricks Gates, Kent S. Univ of Missouri molecules by operating on the top “all” line. You can show the crystallographic unit cell by selecting S -> cell (this is typically not helpful to me. Move on to the next step to find the symmetry pair).
You must manually determine what the correct biological dimer pair by undisplaying successive molecules by clicking on their names in the menu. Note that it is not always obvious which molecule is the correct pair, even to people who have studied a protein for years. You must use your best judgment.
-Undisplay them all by clicking on the all entry, then turn on the original molecule and then go down the list… one will “look right”.
Displaying the “interaction diagram” for a ligand. Go near the bottom of the “Summary” page in the pdb (this typically the first page you land on). Find the window entitled “Ligand Chemical Component”. Look for the “Interactions” heading. Click on the window to see the interaction diagram. At the bottom of the image click “download” to capture a .png file that you can save and open with “preview” (on a Mac).
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)
Pymol tips and tricks Gates, Kent S. Univ of Missouri
• Building In Pymol. Only useful for visualizing “thought experiments”… does not generate reliable, energy-minimized (realistic) protein structures.
(Need a three-button mouse for this, SWITCH MOUSE TO 3-Button EDITING MODE!)
Moving waters and ligands:
Moving waters and ligands is easy. Just remember to set mouse into editing mode first!
For atomic waters, just CTRL-left-click and drag.
For multi-atom ligands, CTRL-middle click on an atom, and then SHIFT- middle-click on that same atom to drag it around.
SHIFT-left-click on that same atom can be used to rotate the entire fragment.
Moving entire loops:
In the menus, go to: Mouse -> 3 Button Edit
In the menus, go to: Build -> autosculpt
Sele resn 367-370 (use number range appropriate for your protein)
Control-shift-left-click DRAG… and the whole loop moves while Pymol does its best to keep the bond angles reasonable.
Changing the conformation of a single side chain. Rotating about a single bond:
In the menus, go to: Mouse -> 3 Button Edit
Control-right click on bond that you want to rotate. (or double-right-click)
Then control-left click… DRAG the mouse after “grabbing” one of the substituents on the end of the bond… and the bond (and its substituents) will rotate.
Moving a single atom within a larger structure
In 3-button editing mode, double-click-and-hold on the atom… then drag it where you want it!
Drawing a new bond:
In 3-button editing mode, left-click on two atoms. Then under the “Build” menu select “create bond”.
Pymol tips and tricks Gates, Kent S. Univ of Missouri
Deleting a bond:
In editing mode, select the bond using Ctrl-right-click, then either “unbond pK1, pK2 or hit Ctrl-D
Deleting an atom
In 3-button editing mode: left-click on an atom then hit “Crtl-D”
Building a carbon chain
In 3-button editing mode, select a hydrogen atom by left-clicking on it, then hit: “Crtl-C”…this adds a CH3 group. Then, select a hydrogen atom on the end of the growing chain and hit Crtl-C again, etc.
Manual Docking in PyMOL
1. Open the small molecule pdb file.
2. Go to the File menu and open the macromolecule pdb file. Now both players are in the viewing window.
3. To selectively move the small molecule into position: Switch to 3-button edit mode, and:
(a) shift-center click moves the molecule in x-y plane
(b) shift-right click moves it “in and out” on z-axis
(c) shift-left click rotates the small molecule.
(with no-shift the entire ensemble can be rotated etc.)
4. To save files as a pdb (instead of a PyMOL session, for example). Type: select all in the command line. Hit “enter”. Then, in the A (action) menu for the “sele” you just created, pick “rename selection”. A line appears in the viewer and you can type in the name. Hit “enter”. Then, go to: File menu -> Save Molecule -> Find the one that you just named on the list and Save it.
• Altering the properties of individual atoms in the structure (color, etc). In 3- button viewing mode, right-click… a menu appears on top of the atom. In this menu, under heading of “atom” you can color, show, label, etc. In 3-button editing mode, command-right-click… menu appears.