Python Molecular Viewer

PMV 1.5.6 Coming Soon

2011-01-05T11:52:00.000-08:00

A release candidate for PMV 1.5.6 is available on mgltools.scripps.edu. I have been using this new PMV for some time. It is really nice. The new dashboard, lighting and clipping are all very well improved. It seems to run faster too. Give it a try.

Kill the shine.

2010-08-23T15:39:00.000-07:00

Do you ever get annoyed by how shiny molecules are? Every picture of a molecule I see shows a shiny shiny molecule, like it was made of alien-space-age-nasa-plastic. Here I show you how to kill that shine, making a dull earthlier look.

Easy to do: decrease specularity value to 0.08.

1. Open Deja vu. Select the 'Light' tab. Select 'Light Colors' box.

2. Set the drop down menu to "light 1- specular"

3. Adjust the Value from 80 (default) to 10 or below.

There's a lot of cool effects to be achieved by adjusting the values and colors of the various lights in the 'Light Colors' menu. Poke around to get a unique look.

Bonus: when you have a look you want to save, Bookmark it! In Deja vu, select 'Bookmarks' tab and click 'Save Representation'.

Calculate Volume

2010-08-20T16:44:00.000-07:00

Quick: what is the volume of this molecular suface?

Here I present a simple method for calculating the volume of a geometric object in PMV.
1. Open Vision.
2. Load the Visualization Library.

3. Drag down the 'PolyhedronVolumeArea' node from the mapper menu and the 'Choose Geom' node from the filter menu in the Visualization library. Drag down the 'PMV Viewer' node in the PMV library. Drag down the 'PopUpMsg' from the Standard Library.

4. Arrange them: PMV Viewer to Choose Geom to PolyVolArea to PopUpMSG. See picture below:

Be sure to choose the geometry you'd like to calculate the volume for.
Here, I have chosen the molecular surface.

5. The volume will appear in the Python IDLE Shell.

Note: units are in Angstroms.

Measure Distance in PMV

2010-08-20T11:33:00.000-07:00

Antibody molecule 1igt, with a wingspan of 152.411 Angstroms, or 15.2 nanometers.

1. Under 'Picking Commands', select 'measureDistanceGC'.

The 'Picking Commands' icon is a pointing hand in blue.

2. Select the two atoms you wish to measure the distance between.

Note: Units are Angstoms.

Ambient Occlusion in PMV

2010-08-19T11:37:00.000-07:00

Antibody 1igt with Ambient Occlusion from PMV by Jon Huntoon

From wikipedia: "Ambient occlusion is a shading method used in 3D computer graphics which helps add realism to local reflection models by taking into account attenuation of light due to occlusion. Ambient occlusion attempts to approximate the way light radiates in real life, especially off what are normally considered non-reflective surfaces.
Unlike local methods like Phong shading, ambient occlusion is a global method, meaning the illumination at each point is a function of other geometry in the scene. However, it is a very crude approximation to full global illumination. The soft appearance achieved by ambient occlusion alone is similar to the way an object appears on an overcast day."

To achieve this sophisticated look is mostly unattainable in other viewing software. But PMV makes it painless. Here's how:

1. Open Deja Vu
2. Select Ambient Occlusion

3. Select the geometries you'd like to have ambient occlusion applied to and then click 'Add'.

4. Select cavity darkness and overall brightness (I left these settings default).
5. Click Compute.

That's all. Sit back and watch the computations chug away. My rendering took about 2 minutes on a new iMac. The other cool thing about this is that once the shadows are calculated, they remain. You don't need to recalculate every time the camera moves like you would in other 3D viewers. Have fun!

Here's what a secondary structure looks like with ambient occlusion turned on.

Ambient occlusion on secondary structure.
Note: the stick-and-balls didn't get rendered.

BONUS: In Deja Vu, select 'Scene Antialiasing' and increase the value to at least 8 for cleaner edges.

-Jon Huntoon

Distinct Molecular Surfaces Per Chain

2010-06-17T16:37:00.000-07:00

How you decide to distinguish between chains in a molecule is really up to taste, but I think there is room for improvement in legibility. Most scientists distinguish chains by color. I do too. But we can go farther, and perhaps, do better.

By default, molecular surfaces are calculated with disregard for individual chains:

This is actually more true to 'real life' or 'in situ'. The water molecules defining the surface of a protein have no regard for chains. They simply pass over. But we operate 'in silico', and afforded the opportunity to distinguish with clarity between the molecular surfaces of chains. Perhaps for the better in the end for discovery- or at least another arrow in our quiver.

Here is a side by side comparison:

I think it is clear from the screen shots above that calculating the molecular surface per chain can be a positive augmentation of the representation.

So, without further adieu, I present the simple trick:

1. While in the computeMSMS popup menu, de-select the 'Per Molecule' check box.

2. In that same menu, be sure to rename the 'Surface Name' for each chain.

That's it!

Another quick tip is that you can reach the ComputeMSMS menu by right-clicking the radio buttons in dashboard:

Enjoy!

JON HUNTOON

Aligning Small Molecules

2010-06-07T11:41:00.000-07:00

From there: to here:

Aligning two small molecules is useful and necessary when studying the similarities of form and character of two distinct molecules. Here's one way of doing that in PMV.

1. Select COMPUTE--> SUPERIMPOSE ATOM PAIRS.

2. Select ADD PAIRS.

3. Turn the BY STRING mode on. You could do this by picking atoms by hand as well. But I find the selecting by string is faster if your molecules have enough similar points (3).

4. The two molecules that I am aligning are methionine and glutamate. I know that they share at least their backbone atoms and the beta carbon "CB". All I need is 3 atoms for an alignment, so I just type "backbone" under the ATOM heading for the REFERENCE and MOBILE nodes. Note that the reference molecule will stay put, while the mobile molecule will be aligned onto the reference molecule, as you might expect.

Also note that by clicking SHOW you will see little blue and red stars over the reference and mobile atoms.

Click OKAY.

5. Now click CREATE PAIRS in the superimpose window.

6. Your molecules should be aligned and you can DISMISS the "pairwise superimposition" window.

Have fun,

JON

Making David Goodsell like illustrations.

2010-04-27T16:53:00.000-07:00

David Goodsell as you may know, is an exceptional artist and brilliant communicator. His watercolors have been published in magazines, journals, and books (The Machinery of Life, Bionanotechnology: Lessons from Nature) and hung up in galleries and exhibits around the world. He writes a monthly column for the Protein Data Bank (PDB) called 'Molecule of the Month'.

Lucky us, PMV has an auto 'David Goodsell' feature.

1. Firstly, there is the "DG Colors" under the color menu. This coloring is similar to atomic but the intensity of the red and blue on oxygens and nitrogen respectively corresponds to the charge of the residue upon which the atom resides. For example, a highly negatively charge oxygens on glutamate will be deep red, where as the less negatively charged oxygens on threonine will be pink. Conversely, the strongly positive charged nitrogen upon the lysine will be dark blue while the less positive nitrogens on histidine are sky blue. A clever coloring scheme that incorporate charge and atom property is one way in which the David Goodsell style conveys so much information without becoming too busy.

2. Now that your models are colored according the custom DG scheme, it is time to emulate the subtle beauty of his water colors. Turn on the 'cartoon mode'.

adjust if you wish:

3. Now you are officially David Goodsell-esque. The last recommendation I have is to increase the anti-aliasing to at least 4. Beyond 8, the anti-aliasing tends to suck too much CPU power.

ENJOY!

Visualizing the Solvent Accessible Surface (SAS) and Solvent Excluded Surface

2010-04-14T14:46:00.000-07:00

What is the difference between the Solvent Accessible Surface and the Solvent Excluded Surface (SES)? And how can I visualize the Solvent Accessible Surface?

The difference is that in a SAS, the surface is drawn from the center point of the probe radius, while in a SES, the surface is drawn from the touching point of the probe radius.

The SES is your typical molecular surface as seen in PMV's MSMS or PyMol (again MSMS), Chimera, Jmol and others. It is also known as a Connely surface. Luckily for us, PMV utilizes Michel Sanner's Molecular Surface (MSMS) algorithm which is generally considered to be the fastest SES calculator.

1. To create an SES, simply goto Compute-->Molecular Surface-->'Compute Molecular Surface'. Use the defaults or change them to suit your need, and click 'okay'.

Easy-peasy, lemon-squeazy. Now, to understand that the SES is a tighter surface than the SAS, we can look at the CPK Sphere representation with the SES (pink, semi-transparent) draped upon the atoms:

Notice how the probe radius really wedges up and along the surface atoms for a snug surface:
Now, the Solvent Accessible Surface (SAS) is created in a different manner.

1. Open Vision, Load MolKit library, and drag down the MSMS macro. Connect your molecule and the PMV viewer.

2. Double click the MSMS macro to open it.

3. Right-click to delete the Green and Blue lines connecting the 'MSMS triang.' node to the 'indexed polygons' node.

4. Drag down two 'ArrayFunc2' nodes and one 'dial' node from the green 'Standard' menu. Connect them as shown below and set the dial to 1.5:

5. Double click the 'MSMS' node inside the 'MSMS macro' node and adjust the density to at least 6.0.

6. Finally, click the lightning bolt a time or two and you should now have the solvent accessible surface, visualized. See how much fatter it is than the SES? Look below:

Here is SAS (slightly-transparent blue), SES/MSMS(slightly-transparent pink), and CPK Spheres (colored by atom) all super-imposed:

SAS colored by David Goodsell coloring:

Bonus:

1. To calculate the SAS and SES area, simply goto Compute-->Molecular Surface-->'Solvent Excluded and Accessible Areas'.

The area listed is in square Angstroms.

**The SAS are correlates to the de-solvation energy.

Solvent Excluded Surface and Solvent Accessible Surface

2010-04-14T10:59:00.000-07:00

Solvent Excluded Surface (SES) and Solvent Accessible Surface (SAS)

-how to calculate the SAS and SES area

-how to colorize SAS or SES residues

-how to list the residues of SAS or SES

1. To calculate the SAS and SES area, simply goto Compute-->Molecular Surface-->'Solvent Excluded and Accessible Areas'.

The area listed is in square Angstroms.

2. To colorize the residues involved in a SAS or SES, goto Color-->by Property-->

Choose the Residue property level. Select SAS or SES area. Be sure to also click the '>>' box to ensure the color is placed along the full spectrum of residues.

If you click 'edit', you can edit the color spectrum along the residues indicated by the y-axis.

3. To get a relevant list of the outward bound residues of the SAS or SES, that is, the residues colored green or yellow or red in the above figures, you must open the python shell.

Type: "mol=self.Mols[0]", enter.

Type: "list=[]", enter.

Type: "for res in mol.chains[0].residues:)", enter.

It should be tabbed over.

Type: "if res.sas_area > 70.0 : list.append( res.full_name())" , enter.

By the way, 70 is an arbitrary number that indicates a depth of surface penetration.

You should get plenty of blue ink. If you get red ink, you probably have a typo.

Click on the image to zoom in:

Load Multiple Molecules Simultaneously

2010-04-07T10:06:00.000-07:00

This is one method. There are many. Specifically, this is useful for opening multiple pdb or pdbqt files at the same time. People who are docking or doing molecular dynamics (MD) use scripts like this all the time. This is just one....

1. In PMV, open the Python Shell.

2. Type "import glob", hit enter.

3. Type "fl = glob.glob("/Users/yourUserNamer/MoleculeFolder/*.pdb")", hit enter. The asterisk tells PMV to find and use anything ending in ".pdb"

4. Type "len(fl)", hit enter. This is a check that your script is working. What appears afterword should be a number- specifically the number of PDBs you

wish to import. In this example, I am loading 15 molecules.

5. Type "for x in fl: self.readMolecule(x)", hit enter. A string of blue should show up indicating each loaded PDB file.

Then choose you representation and enjoy!

Spin, Bounce, Oscillate

2009-10-29T11:06:00.001-07:00

This is how you make your molecule twirl, bounce or oscillate.

1 Open DejaVu.

2 Select Spin Settings.

3 Click Spin button to engage spinning.
4 Adjust using the Vector axes arrows.

Get a physical Model! Molecules in your Hand! Easier than PMV!!!

2009-10-12T10:24:00.000-07:00

All you need is a PDB and an idea and we'll build an actual three-dimensional physical structure you can hold in your hand and pass from person to person. Actually we can use almost any file format to create your molecular model. Also, you may build your own model in PMV or pymol and send the session file our way.

The cost of these models is determined by the volume of the model, the amount of Superglue used to hold it together, and the time it took to make. That is, $5/cubic inch, $10/ounce of superglue, and $25/ hour.

Contact Jon Huntoon by phone (858) 784-2751 or by email huntoon@scripps.edu. Everything we make is custom. A normal model will take somewhere between 1 and 10 hours of modeling time, 1 to 50 cubic inches of material and 0.5 to 5 ounces of superglue, putting the price range at $50 to $500 most of the time.

Please note there will be a 89.5% overhead fee for all models made for researchers outside of The Scripps Research Institute.

Build A Virus

2009-05-13T14:02:00.000-07:00

Don't try to load that entire biological subunit, a whole virus file could contain a million atoms. You're going to crash your computer or at best move very slowly.

--This is for viruses with icosahedral symmetry similar to poliovirus and rhinovirus. For other icosahedral symmetries, some modifications may need to be applied.--

So here's the best thing to do:

1. Load your desired molecule. I am using the great 2plv, or poliovirus protomer. Poliovirus is a pretty simple structure, as you will see.

2. Open Vision, by clicking the button left of the sunglasses.

3. Load the SymServer Library from Libraries--> Load Libraries--> SymLib

4. From the PMV tab drag down your molecule's node and the 'set instances' node onto the blank canvas.

5. From the 'SymServer' tab, drag down the 'Icosahedral 1' node onto the canvas.

your map should look like this now:

6. DoubleClick the 'Icosahdral 1' node. Connect the 'input Ports' node to the '5-fold' node (blue box to blue box).

7. Connect your molecule's node to the 'Set Instances' node (purple oval to purple oval) and connect the 'Icosahedral 1' node to 'Set Instances' node as well ( blue box to blue box)

You should be golden now! You can make surfaces and color or anything you want, and the great thing about it is that your really only doing this to molecule instead of 60! This way, hardly any memory is used up!

-Jon Huntoon

Read an STL file

2009-05-07T11:39:00.000-07:00

Here's how to read a Stereo-Lithographic file (.STL). STL files are a simple list of XYZ coordinates of vertices. They are geometry. If, for whatever reason, you want to import some shape, like a torus, or even and molecular surface you can! First you need that .stl.To save a .stl file in PMV, simply goto File--> Write--> Write STL. Or if you want some foreign shape use your 3D modelling program like Google SketchUp or Maya to save an stl.

1. Open Vision.

This button:

2. In Vision, load the Visualization Libarary, 'vizlib', under Libraries-->Load Library-->vizlib.

3. a Drag down the 'Read STL ASCII' node from the 'deprecated' list in to the blank canvas area.

b Drag down the 'PMV Viewer' node from the PMV tab under the PMV list.

c Double-click the 'Read STL ASCII' node and load your STL file.

d Connect the two nodes by dragging a line from the bottom blue circle of 'Read STL ASCII' to the top red box of 'PMV Viewer'.

Now, that torus or whatever should be present in the viewer.

BONUS #1: This geometry will be listed in the DejaVu GUI.

BONUS #2: You can connect the torus to a pdb by binding the geometry to the molecule under '3D Graphics'--> 'Bind Geometry to Molecule'. Then you can color that torus by atom type proximity just as you would any other surface.

-Jon Huntoon

Select the HET Atoms

2009-05-01T11:19:00.000-07:00

Want to select small molecules and co-factors? The atoms that aren't part of standard residues, like drugs, cholesterols, Zn atoms, and all else?

Things like this:

HETATM 2185 O6 MAN A1310 78.725 55.327 98.231 1.00 81.20 O

HETATM 2186 ZN ZN A1311 62.745 46.321 102.600 1.00 38.48 ZN

HETATM 2187 CL CL A1312 59.817 29.875 99.087 1.00 40.97 CL

HETATM 2188 CL CL A1313 41.111 19.647 77.717 1.00 38.39 CL

HETATM 2189 O HOH A2001 59.085 17.513 98.258 1.00 65.67 O

from your PDB file...

Here's how:

1 To select the HET atoms, goto Select--> Select from String.

2 Under the 'atom' field, type: lambda x: x.hetatm == 1

3 Click 'Add' and your HET atoms will be selected.

-Jon Huntoon

Opacity

2009-04-30T11:58:00.000-07:00

Sometimes you need to see what's below the surface. Here is one way: lower the opacity of the surface... & here is how:

1. Start with a Molecular surface, and a ribbon. Calculate these under Compute--> MSMS, and Compute--> Secondary Structure-->Ribbon. Color the Ribbon by Secondary Structure.

2. The surface is now hiding the ribbon. To see both the ribbon AND the surface, Open the DejVu GUI.

3. Select the MSMS-MOL surface.

4. Under 'Material' deselect the 'inherit' property and then click the 'Front' box.

5. At the bottom of this Material Editor, there is a slider that controls opacity. Lower the opacity to about 50%.

6. Now you can see both your ribbon and your surface.

-Jon Huntoon

Electron Density Map

2009-04-28T17:16:00.000-07:00

Here is how you can read and display an electron density map. These are important to look at if you are to be critical of a particular PDB structure.

1a Load PDB

1b Download the corresponding CCP4 file from PDB.

2a Create a Vision Network.

(middle button, boxes & lines, not the sunglasses button)

2b Load the Vis and Vol Libraries from Libraries--> Load Libraries....

2c Drag the following 'nodes' on to the blank 'canvas':

- 'Read Any Map' (Load CCP4 here) -from Vol Library (grey)

- 'Sample' (use a level 3 or two) - from Vol Library

- 'UT iso-contour' From Vol Library

- 'Ind Polygons' -from Vis Library (yellow)

- 'PMV Viewer' - from PMV Library (purple-ish/blue?... hmm. Periwinkle!)

(it helps to use the search box to find these nodes)

Connect these nodes by dragging lines from the output ports (bottom square things) to the input ports(top square things) (colors should correspond [mostly]):

3 Double-click the UT iso-contour 'node' to see the isocontour graphs. Looks like this:

4 Drag the black vertical line to Pick an iso-value that suits your purposes. It will be hairy, so you may want to...

5 Open DejaVu (it's the left-erly button with a cube, sphere and pyramid) to adjust opacity and or clipping of the IndPolygons geometry you just created!

And you can end up with something like this or (probably) better. Explore around. Have fun. Get good.

Jon Huntoon

ADT/MGLTools freezes on my Intel Video Graphics Card!

2009-04-17T14:58:00.000-07:00

Apparently,

Intel launched those cards prematurely. They weren't ready for Vista's
high-end graphics uses. You should try downloading the latest driver
from Intel.

Also, try downloading MGL 1.5.4. This is the most up-to-date. It's
your best bet even though it's beta.

Unfortunately, this may not work. You may need to buy a better
graphics card. nVidia and ATI are the best.

Another last-ditch attempt is to install linux and use the linux
version of MGL tools.

It's a challenge developing software that is completely free. Free
libraries can be out of date with hard ware, and hardware drivers can
sometimes ignore old(free) libraries. MGLTools will move to python 2.6
that should fix many of these problems, but the implementation will
take a couple months.

Create Bonds On The Fly

2009-03-06T15:51:00.000-08:00

Say you load a pdb file and discover (to your dismay) that the heme's iron is not bond to the surrounding carbons. Here's how to add bonds between the atoms (to make it proper).

1. Click Picking Commands. It's the hand pointing to the upper left.

2. Choose 'addBondsGC' from the first drop-down menu that appears.

3. Click the unbound atom, a yellow ball should appear upon it along with a label.

4. Click the atom to which you think it should be bound. A line will be drawn betwixt the atoms.

5. Repeat until proper affect achieved.

note: if you would like to keep these changes, be sure to save the molecule with the connect records as well as the 'UserDefined' bond types:

Fwd: Subcribe

2009-03-06T15:17:00.001-08:00

If you would like to subscribe to this blog, please either post your email or send it to huntoon@scripps.edu, and I will sign you up, so you can get tips as soon as they are posted.

Jon Huntoon
Molecular Graphics Lab
The Scripps Research Institute

Color Map Tip

2009-03-06T14:43:00.000-08:00

To make nice, straight lines for your color map, hold down the command/control key while you click and drag upon the color field. ;)

Adpative Poisson-Boltzmann Solver, APBS, continuum electrostatics

2009-03-06T14:11:00.000-08:00

Need some electrostatics? Easy.

1. Load Molecule.

2. Goto Compute-->Electrostatics-->Compute Potential Using APBS

This will open a window with a lot of blue ink. When the scripts finish chugging, click OKAY and your molecule should have hydrogens added to it.

3. Goto Compute-->Electrostatics-->Map Potential to Surface

And there you go. Simple, right? You could make it harder if you want.
You could change the colors by double-clicking on the color scale-bar in you viewer.

And there are plenty of other settings to play with along the way. The best way though, is to just use the standard settings, which will yield similar results as the other programs. That's the beauty of PMV, you can keep it simple, but you can also tweak the model ad nauseam if you wish.

Control Your Mouse Buttons!

2009-02-09T12:14:00.000-08:00

Have you tried playing with the settings under File > Preferences > Bind Actions to Mouse Buttons?

In this widget you can control which button does what. Take Control!

Emphasis On the Utility of Using the Delete Key

2009-02-09T10:34:00.000-08:00

Really, this is so handy. Programs, oddly enough, didn't use to have this functionality. You want a program to work how you expect, and this is one feature that delivers. If you want to delete some selection, select it, and the hit the delete key. Easy. it just works. I am trying to figure out a use for the arrow keys. They are good keys! They currently languish upon the keyboard unused. Maybe you all have some good ideas for some so-called 'hot-keys' that can be incorporated into PMV. I sit right next to a bunch of the PMV programmers, and they are able and willing, we just have to give them good Ideas.

Labels

2009-02-09T10:23:00.000-08:00

Want labels? There are many labeling schemes you can produce in PMV. So many, that, you really have to just sit down and play with it for a while to see all the possibilities. Here I will show you how to label residues by their name.

1. Make a Selection. Make sure you have the right picking level. If your picking level is set to atoms, then atoms will be labeled, but we want residues labeled so I have changed the picking level to residue.

This can also be done under Selection --> Set Selection Level.

2. Go to Display --> Label --> by Property.

3. Make any adjustments like what color you want or the font using the Label Settings tab and hit okay.

You should be golden now:

reset - normalize - center

2009-01-28T11:59:00.000-08:00

Do you ever lose sight of your molecule? Can't find it? Or its just askew?
Try typing R N C, which resets its position, normalizes it and centers it. Voila!
Another option consider is using the center on nodes option. This allows you to choose a center of rotation.

Ask me anything.

2008-12-16T17:24:00.001-08:00

Ask me anything, and I can help you. Especially if your questions are easy. :) I have worked in the Molecular Graphics Lab at Scripps Research for nearly 5 years using PMV for most that time. If there is something you want to do, and it seems like it should be easy, it probably requires some little trick to get working and I will tell you how.

email me, Jon Huntoon, huntoon@scripps.edu

Toggle Depth for Instant Light.

2008-10-20T17:23:00.000-07:00

Here is a real quick trick: if you want the lighting to instantly be bright on your object (by eliminating the depth cue), hit the "D" key and voilà.

1. Press "D" key.

Clipping Plane

2008-10-20T10:47:00.000-07:00

A clipping plane is an excellent way to explore the interior of a protein structure, while also giving reference to the exterior. Sometimes, you can even find complex tunnels that bore into the interior of a protein. To clip in PMV:

1. Create Molecular Surface by going to Compute--> MSMS

2. Click on the DejaVu button.

3. In DejaVu, turn on the clipping plane.

4. In DejaVu, toggle between Clip and Object under "Mouse Transforms" to manipulate the clipping plane and the object alternately. Your 3 button mouse translates, scales, and rotates the clipping plane the same as it does your object.

5. For additional clarity, modify the object's 'Back Material' in DejaVu under Object->'Back'

6. Additionally, you can select the individual object to be clipped, like the molecualar surface and leave in tact features such as a stick and ball representation of a heme group.

Selection by Distance

2008-10-17T11:42:00.000-07:00

A very nice feature of PMV is the Seletion by 'Spherical Region' which allows you to select atoms within and particular Angstrom radius. This allows you to see the possible interactions of say, a ligand within a pocket in the protein. To do this:

1. Select the atom(s) or residue(s)

2. Go to Select--> SpericalRegion

3. Select 'Current Selection'

4. Hit 'Close' on the dialog and you should have the atoms within the specified radius (usually 5 Angstroms) selected.

5. Now you can color them or highlight them in some other way to make the proximity more apparant.

Background Color

2008-10-16T12:19:00.000-07:00

Changing the background color is simple and can help discern details, please your eyes, or prepare for a publication.

1. Go to 3D Graphics --> 'SetBackGroundColor' and then click away.

Remove Waters!

2008-10-16T09:42:00.000-07:00

Here is how to remove waters in PMV:

1. Go to 'Select'--> click 'Select From String'

2. Type "HOH*" (or maybe "WAT" depends on the PDB file) under 'Residue' and click add.

3. Hit the DELETE key and then click continue on the dialog. OR Goto 'Display'--> 'Lines' and click 'undisplay' an 'OK' if you just want to hide them.

Hydrogen Bonds

2008-10-16T09:31:00.000-07:00

Hydrogen bonds interconnect the turns on a helix and the backbones of a sheet. They also stabilize DNA and RNA. Here is the rundown on how to display hydrogen bonds in a typical fashion.

1. Go to File--> Browse Commands

2. Click PMV --> select 'hbondCommands', click 'Load Selected Module'

3. Select "backbone" under 'Atom' in 'Select From String'

4. Go to Edit--> Hydrogens--> Add

5. Select 'Polar Only' and hit OK

6. Go to Hydrogen Bonds--> Build--> Click "Select Parms and Build"

Click OK on the dialog that pops up.

7. Goto Hydrogen Bonds--> Display --> Cylinders

8. Click 'Set anchors', donors: N, acceptors C, and change the color if you wish as well.

In the Show Hydrogen Bonds as Cylinders dialog you can adjust the radii and length of the bonds as well as toggle them on and off by clicking the individual bonds in the table on top.

Rainbow Coloring

2008-10-15T16:19:00.000-07:00

Rainbow Coloring!

Coloring a secondary structure from its N-terminus to its C-terminus is a useful a popular visualization style.

To accomplish this style:

1. Go to Color-> Color by Property

2. Select what structure you want colored

3. Click 'Residue' from the top Tab and 'uniqIndex'

4. Click the '>>' tab and then okay.

Post # 1

2008-10-15T11:03:00.000-07:00

This blog is about Python Molecular Viewer (PMV), specifically, how to use PMV to make nice models and images. I will be posting tutorials that show how to make the visualizations everybody wants.