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I have used PyMol for years and have done numerous posts related to it. However, that may soon come to an end. The reason being that Discovery Studio Visualizer 2.5 (DSV) is just better. I am still getting used to the program, but wanted to share with you three ways to ’select a region’ to get you pumped up!

1) Highlight amino acid sequence
You can display the amino acid sequence by Sequence -> Show Sequence
When you highlight on the sequence – the structure is also highlighted.

The structure can be viewed on the other tab (I really like having tabs instead of separate windows):

2) Lasso
Simply draw over the region you would like to be selected.


3) Clicking
An atom can simply be selected with the pointer and with a right click, pertinent information will be displayed. In this example, I have double clicked which highlights the residue.
Four clicks will select a chain.
Six will select the entire structure.

Once a selection is made you can then easily make adjustments using the display tab (I previously mentioned this here).

*Bonus*
4) Ligand
DSV has a ligand script so that can VERY quickly generate the following figure
Scripts -> Ligand Interactions -> Show Ligand Interactions with Atoms:

A couple of changes and you can have a publication quality figure in no time.

I regret to inform you of the passing of Dr. Warren Lyford DeLano. Warren passed suddenly Tuesday morning on November 3rd, 2009.

Although the crystallographic community is small. I did not have the pleasure of knowing Warren personally. However, I wanted to express my sincere appreciation for his scientific contributions.

Warren was the developer behind the molecular graphics program called PyMol. I have written numerous posts about PyMol since it is truly one of the best molecular graphics programs.

I have had a love/hate relationship with PyMol, but one thing that I never questioned was Warren’s dedication in helping others. Warren set up his own forum just to help others with questions that they had about PyMol. Warren was also a leader in the open source movement within crystallography.

My wishes sincere condolences to Warren’s family.

A website has been setup by the Delano family. They have asked for all memories be posted at that location, thank you.

Written by Axel T. Brunger
Dear friends and colleagues:

It’s now been over a week since Warren has passed away. We are trying to move toward a permanent way to honor Warren’s memory and what he stood for: Open Source Computational Biosciences and molecular visualization. To do this, Jim Wells and I put together a mission statement with the approval of Warren’s family:

The Warren L. DeLano Memorial Award for Computational Biosciences

This award shall be given to a top computational bioscientist in recognition of the contributions made by Warren L. DeLano to creating powerful visualization tools for three dimensional structures and making them freely accessible. The award, accompanying lecture, and honorium will be given annually in the context of a national bioscience meeting or a Bay Area gathering of computational bioscientists at Stanford, UCSF or UC Berkeley. For the award special emphasis will be given for Open Source developments and service to the bioscience community.

The award selection committee, consisting of experts in the computational and biological sciences, will accept nominations from anyone..

To make something like this happen in perpetuity would take about ~100K for the endowment.

For donations, Warren’s family has set up a tax deductible fund:

Silicon Valley Community Foundation
memo: Warren L. DeLano Memorial Fund
2440 West El Camino Real, Suite 300
Mountain View, CA 94040
tel: 650.450.5400

We hope that you’ll consider making a contribution (not matter how small) in Warren’s honor. Also, please forward this message to anybody who might be able be willing to contribute.

Best regards,
Axel

**Update**
Fred notes:
For those of you who may worry about the future and future availability of PyMol, this is the information I have received from Elizabeth Pehrson (Warren’s wife, DeLano Scientific LLC):

“I would like to reassure all who fear for PyMOL’s future that DeLano Scientific still exists, we are still accepting (and receiving) subscriptions, we are still providing maintenance and support, and I am working closely with some of Warren’s most trusted developers to plan for the future of PyMOL”.

**Update**
Obituary by Axel Brunger and Jim Wells in Nature Structural & Molecular Biology

I will update this post as I hear more information.

The developers at Accelrys are behind Discovery Studio Visualizer 2.5 (DSV) are really pushing the molecular visualization field along. You can download DSV for FREE after a quick registration.

I actually tried to use this program a couple of months ago, but ran into problems because my computer did not meet the minimum system requirements.

I dropped Accelrys a quick note on their blog and they were able to connect with someone who was able to give me a hand (thanks again, Luke).

My reason for wanting to play around with this program is my need to find a simple and efficient way to create figures for presentations and publications. The program contains many other capabilities related to small molecule libraries and pharmacophore modeling, but those will have to wait.

A couple of items that I like right from the start:
1) I love that the program runs from one window and utilizes tabs

2) The layout can be customized by a simple drag and drop (ie. you can have your tools on the top, to the left or right, on the side bar, etc.)
3) You have the option for a full screen view that saves some squinting
4) I am fan of GUIs and not typing commands – DSV has really come through in that department
5) The Display Style window is really easy to use and check out the number of options, awesome.
One suggest is to add the ability to move the protein while the Display Style window is open
6) Check this one out called Line ribbonsI don’t think I would ever use it in a presentation or paper, but still think it looks cool.

The reason that I am such a fan of Pymol is its capability of producing high quality images. I selected the Ultra high resolution in DSV and exported it as a png file.

Here are two pictures side (left Pymol) by side (right DSV) both are 564×507 pixels.

I found it strange how the program displayed bonds such as the double bonds from carbon to oxygen. The reason being that this is usually not shown in other visual programs. I am guessing there is some way to turn it off, but by initial reaction was wow – look at all these dual conformers
Overall, definitely worth downloading. I would love hear your thoughts on how the DSV compares to your favorite visualization program.

1) Download your coordinate file, if applicable (if you are using an existing structure the coordinate file is probably located in the Protein Database).

2) File –> Open, the PDB file

3) The structure should appear

4) Then click on the H and select everything

5) Then click on the S and select cartoon

6) The cartoon of your PDB should now appear

7) When using Pymol for Figures or presentations it is often best to set the background as white
Display –> Background –> White
Note: If you would like a different perspective, rotate the molecule before the next step

Click on Ray button (upper right) in the PyMol Tcl/Tk window

1) Go to the Electron Density server and enter you desired PDB code (1c8u in this example)


2) Download the coordinates, followed by the map in CCP4 format


3) Extract the files that you downloaded
(7-zip will work for windows if you do not already have it installed)
**Rename using the term map: example) 1c8u.ccp4 renamed to 1c8u.map.ccp4

4) Start PyMol and open the pdb and map files (File -> Open)


5) Display the map by clicking on the ‘A’ for actions then mesh followed by selecting your desired mesh level – as shown above (I did 2.0 in this example)

-Below: if you look at the upper right corner you can see what is displayed by if it is highlighted (light gray) in the PyMol window (in this case 1c8u.map is off)


6) Enter the information available on the PyMol Wiki into the command line (enter everything left of the # symbol)

select site, resi 39-50 # residues that are displayed for viewing
isomesh map, 1c8u.map, 2.0, site, carve=1.6 #display the map around the selected residues (change 1c8u.map to correspond to how you named your .map file)


color grey30, map # sets map to 30% gray
bg_color white #sets background to white
set ray_trace_fog, 0 #turns off raytrace fog–optional
set depth_cue, 0 # turns off depth cueing–optional
set ray_shadows, off #turns off ray-tracing shadows

I then zoomed in on one of the selections then showed ‘S’ ’sticks’ in the PyMol window.

7) Click on ‘ray’ for ray tracing then followed with ‘color grey30, map’ since the mesh looked black (note again what is toggle on and off in the upper right)


Finally, you can add labels using GIMP or Photoshop

Don’t forget to cite PyMol

If you would like to learn how to easily make a movie using PyMol check this post out.

I realize using the term easy and PyMOL together (at least when dealing with the free version) is somewhat of an oxymoron. So there must be a coveat which is that if you want to make a movie with PyMOL you need to get eMovie. If you haven’t already wasted 6 hours trying to figure out how to make a movie with PyMOL alone feel free to comeback.

Welcome back, so once you have installed eMovie (make to put the files in the correct location as described on the download page) the next step is to start up PyMOL.

If installed correctly you should see an additional GUI (at right) as shown below:

My goal here is to give a basic introduction that will yield a movie that rotates a protein in a full circle. The eMovie website has more advanced examples, but they are not as step by step as shown here.

Usually during a presentation the protein is shown with a white background. This can be done in PyMOL via the PyMOL GUI under Display -> Background -> White

eMovie GUI click Scenes (views, appearances)
Create new scene/Save scene…
name: rotation
click on Rotation in the eMovie GUI (right below Scenes on the GUI)
Axis: y
Degrees: 360
Start Frame: 0
Action Length: 120
-click ok

click Add stop (in GUI)
Insert stop frame: 120

You can now view how the movie looks so far at this point by using the PyMOL GUI click Play (roughly the center button in the GUI)

Tip: save often because if PyMOL or eMovie freeze your settings will be lost (this happens quite frequently).

eMovie GUI click View Storyboard
click on Stop
Deleted selected action
*you must remove the stop before exporting*

eMovie GUI click Export eMovie
(set GUI viewing window to the size of the movie for viewing)
This notice is especially critical if you have different views. You need to make sure that the size of the PyMOL window is consistent. I would recommended making your entire movie in one sitting to avoid a sizing issue.

Tip: If you are going to do multiple views then name them in alphabetical order – in the order in which they appear. For example, you want to do a rotation then zoom – name the rotation frames arotation and bzoom for the zoom (r is before z therefore it would be the right order without the a/b prefix, but hopefully you get the idea).

As a personal preference, I set up a separate folder for each movie which I then export the frames from eMovie into.

Load the rendered images into Adobe ImageReady CS2
File -> Import then select the folder containing the images

You can highlight all the images and adjust the time to 0.1 seconds for smooth playing. Also if you want a delay such as from a rotation to a zoom you can increase the time on that particular frame.

File -> Export original document
Quicktime Movie (may want to consider the type of computer the presentation will be presented on)
Compression settings jpeg -> Best (quality)

Tip: Powerpoint reads the location of the movie files that have been inserted. Therefore you should load the frames on the flash drive with your talk and then save them. This should help avoid the ‘I am not sure why this movie isn’t working’ during your presentation.

Don’t forget to cite PyMOL and eMovie.