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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.