What will become of PyMOL?

Schrödinger announced several days ago that it has reached an agreement with the estate of the late Dr. Warren L. DeLano to continue the development, support, and sales of the PyMOL software package.

PyMOL is well known to all of us in the field and is perhaps the most widely used and loved molecular visualization tool. According to the announcement, prior to his unexpected passing Warren DeLano, had been working closely with Schrödinger for over a year, and in constant discussions concerning ways to progressively integrate the companies’ products. Warren’s wife said: “I know this is what Warren wanted for PyMOL’s future.”

Tom Stout added on the CCP4BB that Jason Vertrees that has been working closely with Warren for the past several years as a co-developer has agreed to join Schrödinger.

However, a quick search on twitter shows a range of feelings towards this acquizition:

What do you think this means for PyMOL’s future ? Tell us in the comments.

Written by Nir London in: News | Tags: , , , ,

What is your favorite molecular viewer ?

One of the main tools of the structural biologist (computational or experimental) if not, THE main tool, is the molecular viewer he uses. There are various viewers available, but usually each of us, at a certain point at his career, chooses a specific one and specializes in it. It becomes a way of self expression, to the point that using a “non-native” viewer is like talking in a foreign language. (How do I select only the polar atoms within 4.5A of chain B and color them CPK in this awkward viewer ?!?!?! On MY viewer it would take me a second!)

We want to hear what is YOUR molecular viewer of choice. Each viewer is optimized for a different set of tasks. E.g. VMD is designed for molecular dynamics, UCSF Chimera integrates many molecular analysis tools, Rasmol is a quick and dirty command line operated little fellow, not producing the nicest figures though, PyMOL creates good looking figures and is highly scriptable (as we demonstrated before in PyMOL scripts), while Jmol is web oriented and easy to embed in web pages.

What is your favorite molecular viewer ?

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There are other software available, please tell us in the comments what’s your favorite viewer advantages and what are the disadvantages of the other “lesser” 😉 viewers.


Molecules on the go – iPhone app.

How many times have you talked to someone at a conference, or in a meeting and tried to explain to him, while hand waiving or napkin drawing, that cool structural feature of your protein? Well, with “Molecules” the hand waving can stop and the finger waving begins.


Written by Nir London in: Resources | Tags: , , , ,

PDB fetcher Google Gadget

Have you ever read a paper, stumbled upon some random PDB id and was itching to see the structure ? maybe play with it for several minutes ? get a general impression ? but, alas, you were too lazy to actually go the PDB and download the structure! Carson Andorf provides an easy solution in the form of a “PDB Structure Viewer with Sting!” Google Gadget. 

Just enter your PDB id and viola you get an image of the structure another click on the image would let you play around with it. Add this to your iGoogle page and you’ll never shun another molecule again. And while your at it, add the macromolecular modeling blog feed to your iGoogle page as well Add to Google  :)

What is your favorite google gadget ? Tell us in the comments.
Easy to use google gadget to view PDBs

Written by Nir London in: Resources | Tags: , , , , , ,

PyMOL scripts

Have you ever tried to represent your protein as a “sausage”-style cartoon, with the tube diameter scaled by values in the B-factor column ? We present an array of useful PyMOL scripts links to solve your problem.

PyMOL is, as defined on its home page: “.. a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation”. Indeed it is one of the most popular molecular viewers out there. One of the main strengths of PyMOL is its inherent scripting abilities. I’m sure that many of you knew that, but have never really taken the time to write such scripts, and why would you ? others have done the job for you!


Written by Nir London in: Resources | Tags: , , , ,

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