Illustrating EFMO fragmentation with Jmol

On Tuesday I am giving a talk and I want to illustrate fragmentation of a protein for the EFMO method.  So I used Jmol to create this movie which I will embed in a Powerpoint slide

The underlying Jmol script is here.  Just paste it in to the Jmol Script Console and record the screen (I used Screenflow, but screencast-o-matic is a free alternative).


This work is licensed under a Creative Commons Attribution 3.0 Unported License.

Computational Chemistry Highlights: recent important articles in molecular modeling

The first (February) issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years.  CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists.  You can read more about it here.

Table of content for the February issue featuring contributions from CCH editors Jan Jensen and Steven Bachrach:

Total Synthesis of Oxidized Welwitindolinones and (-)-N-Methylwelwitindolinone C Isonitrile

Roaming-mediated isomerization in the photodissociation of nitrobenzene

Assessment of Popular DFT and Semiempirical Molecular Orbital Techniques for Calculating Relative Transition State Energies and Kinetic Product Distributions in Enantioselective Organocatalytic Reactions

Regiochemical Substituent Switching of Spin States in Aryl(trifluoromethyl)carbenes

NMR Structure Determination for Larger Proteins Using Backbone-Only Data

Interested in more?  There are already several contributions to the March issue and there are many ways to subscribe to updates.

 

Dancing orbitals

Amazing movie of dancing orbitals (aka charge transfer dynamics) from Felix over at Chemical Quantum Images.

High density energy storage using self-assembled materials

This award winning movie was made by Chris Wilmer, a graduate student at the Snurr group at Northwesten.  I am thoroughly impressed.
Via Wired.

Animations of Unseeable Biology

More animations by Drew Berry

Related blog post
The computational Microscope

Reinventing Discovery: Practical steps toward open science

What can you do if you're a scientist?

I recently finished reading Michael Nielsen's book Reinventing Discovery.  This is not another review of the book (there are many: Google it).  I'll just say it is a well written book on a very important topic, so go buy it now.

Towards the end of the book there is a section entitled "Practical steps toward open science" and one subsection is about what you can do if you're a scientist.  There are some good suggestions, some of which I'd like to expand on here, and I'd like to add some new suggestions as well.  The suggestions are roughly ordered in increasing effort (though not necessarily impact!), together with my own examples (where applicable).

Read the rest of the post over at Proteins and Wave Functions

Chemistry of the future: 3D and augmented reality

Way cool! 'Nough said.

Rotating molecules in Powerpoint - part 2

Animation in Powerpoint
One of the most accessed posts on this blog is Rotating molecules in Powerpoint.  I wrote the post more than a year ago, and had I written the post today it would be different thanks to a great free program called Screencast-o-matic.

The screencast above shows how to use Screencast-o-matic to make short movies of rotating molecules and other molecular animation and include them in Powerpoint presentations.

Jmol in Powerpoint
A lot of people end up on this blog by searching for "Jmol in in Powerpoint" or some similar term.  As far as I know it is not possible to embed Jmol in Powerpoint slides.  It is possible in Beamer, as discussed in this post by Janus Eriksen.

Using Screencast-o-matic you of course record any sequence of Jmol animations, but it will not be interactive.  Personally, I make a web page with my Jmol model, with buttons to control what I want to do and simply switch between Powerpoint and a browser.  I give a short example using this Jmol model in the screencast below.

Blurring the boundary between linear scaling QM, QM/MM and polarizable force fields Part 2

My talk at WATOC 2011.  Slides can be found here

Here's how I made the video: I recorded my talk using the Voice Memo app on my iPhone.  Then I replayed the talk on my Mac using iTunes as I went through my slides on Powerpoint.  I recorded the screencast + audio using Screenflow.

Thanks to Anders Christensen for recording the video.

Summarizing a paper using Prezi and Screencast-o-matic

In a previous post I summarized a paper using two programs: Prezi and Screencast-o-matic.  Both are free and easy to use.  The screencast above shows how I did it. Anyone can do this.

I did this on a mac, so I used the earphones/microphone that came with my iPhone.  The sound is not the greatest, but good enough I think.

The screencast is 9 minutes long, which might be too long.  It's hard to strike a balance between detail and the big picture.  Hopefully, I will improve with time.  Feedback is very welcome.

Update: be sure to check out the comments below

New paper: Ring current effects in proteins

Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts

Anders S. Christensen*, Stephan P. A. Sauer, and Jan H. Jensen*

Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark

J. Chem. Theory Comput., 2011, 7 (7), pp 2078–2084

DOI: 10.1021/ct2002607

Abstract (the paper is summarized in the video at the end of the post)
The ring current effect on chemical shifts of amide protons (Δδ_RC) is computed at the B3LYP/6-311++G(d,p)//B3LYP/aug-cc-pVTZ level of theory for 932 geometries of dimers of N-methylacetamide and aromatic amino acid side chains extracted from 21 different proteins. These Δδ_RC values are scaled by 1.074, based on MP2/cc-pVQZ//B3LYP/aug-cc-pVTZ chemical shift calculations on four representative formamide/benzene dimers, and are judged to be accurate to within 0.1 ppm based on CCSD(T)/CBS//B3LYP/aug-cc-pVTZ calculations on formamide. The 932 scaled Δδ_RC values are used to benchmark three empirical ring current models, including the Haigh–Mallion model used in the SPARTA, SHIFTX, and SHIFTS chemical shift prediction codes. Though the RMSDs for these three models are below 0.1 ppm, deviations up to 0.29 ppm are found, but these can be decreased to below 0.1 ppm by changing a single parameter. The simple point-dipole model is found to perform just as well as the more complicated Haigh–Mallion and Johnson–Bovey models.

The paper Instructions on how I made the video will appear in a future post. In the mean time, enjoy!

ChemDoodling: now in 3D, but not (yet) on the iPad

 

You need Google Chrome or Firefox 4 to view the molecule.

In a previous post I wrote "The 3D version of ChemDoodle Web Components requires something called WebGL, which is not available in standard browsers yet, but should be soon.  You can get access to it now by downloading Google Chrome (BETA)."

Now you just need Google Chrome or Firefox, i.e. if you view this post in the Google Chrome or Firefox 4 browser you should be able to interact with the molecule.  Other browsers should include WebGL soon, and when it reaches Mobile Safari, it should work on the iPad.

This means ChemDoodle Web Components is ready for use in research and education.  It's quite easy to use: see here for installation instructions and here for a simple html example.  Furthermore, "Over the next couple years, we intend to match all functionality in JMol" according to Kevin Theisen.

I note that the ChemDoodle Web Components are open source, so feel free to pitch in!

ChemDoodling on the iPad and the future of interactive chemistry textbooks

Interactive model of morphine

I have bought an iPad!  In honor of this purchase I bring to you this blog's first interactive figure that also works on the iPad (and most other mobile devices).  It is made with ChemDoodle Web Components (a modified version of this page), an open source javascript based toolkit for chemistry, made by Kevin Theisen and co-workers at his company iChemLabs.

Readers of this blog will know that I am quite fond of Jmol for interactive molecular models, but Jmol is written in Java, which is not supported by the iOS operating system that iPads, iPhones, and iPods use - and perhaps it never will be.   This decision by Apple basically means back to square one for interactive chemistry when it comes to the iPad.

I know of just two options for interactive models for the iPad: the Molecules app by Brad Larson and ChemDoodle Web Components (TwirlyMol does not appear to be interactive on the iPad).  The Molecules app looks a bit more three dimensional, but works only on the iPad.  Chemdoodle Web Components should work on most browsers and most operating systems, and a fully 3D version is also available.  The 3D version of ChemDoodle Web Components requires something called WebGL, which is not available in standard browsers yet, but should be soon.  You can get access to it now by downloading Google Chrome (BETA).

It is the Molecules app that is used in the interactive text book from Inkling that I wrote about earlier (thanks again to Henry Rzepa for the info).  But I think ChemDoodle Web Components holds tremendous promise for interactive chemistry textbooks when combined with another new innovation on the horizon: EPUB3.

Epub is basically code that makes XHTML look nice when viewed in an epub reader (such as iBooks), but the current version does not allow for things like javascript, needed for interactivity.  That will change with epub3 and, when combined with ChemDoodle Web Components, should allow us to make interactive chemistry textbooks that can be read on most devices.   It will be an exciting time.

Arsenic and odd life

A recent Science paper describes "A bacterium that can grow by using arsenic instead of phosphorus", and molecular visualization is used to elegantly illustrate the basic idea, a shown in the above screencast (for the whole video visit gizmodo).

Whether the basic idea is correct is a whole other matter: for examples see here and here (be sure to check out the comments).

The Open Science unjournal

In this post I do something a little different than normal for this blog: I introduce a scientific unjournal called Open Science.  It doesn't exist, but it should.
 
What is an unjournal?
An unjournal is to journals what an unconference is to conferences.  To define what an unjournal is, take the first 2 sentences in the wikipedia entry on unconferences and substitute a few words:  "An unjournal is a facilitated, participant-driven journal centered on a theme or purpose. The term "unjournal" has been applied, or self-applied, to a wide range of publications that try to avoid one or more aspects of a conventional publishing, such as loss of copyright, high fees, [list your favorite pet-publishing-peeve here]."

Here are some frequently asked questions (FAQs) about Open Science:

How do I publish in Open Science?
The usual way is to deposit your manuscript on openscienceunjournal.org.  Once you have completed the submission process the paper is given a time and date stamp and the paper is published and open for review (see next question).  While there is a recommended template available for the paper, there is no fixed format.  It is possible to upload all your raw data or link to the data if it is hosted elsewhere.  Experience has shown that this tends to increase the scores (see below) of your papers significantly.

You can also choose to publish the paper on any of the unjournal sites whose contents are linked to openscienceunjournal.org.  These sites are often run by established publishers and offer more user-friendly interfaces, but may require a fee and may ask you to give up your copyright (though the content is open access by definition).

Is Open Science peer reviewed?
For a publication in an unjournal such as Open Science the question should be: is my article in Open Science peer reviewed?  That is in large part up to you.  The paper is open for online, non-anonymous, and completely transparent review and you have 2 months in which you can change the content of the article in response to the comments.  After the 2 month period you cannot change the content, but you can of course respond to new comments online.  For very serious criticisms you may want published a new Open Science article to respond.

It is up to you to solicit reviews, though any published author of a peer-reviewed paper (defined below) can review your paper during the 2 months review process.  Based on our experience only well-written and well-presented articles on scientifically interesting questions get reviewed.

An Open Science article is neither rejected nor accepted at the end of the review process.  Instead it receives an initial score (see next FAQ).  Obviously, any paper that does not generate a single review (or is reviewed but gets an initial score of 0) is not considered peer reviewed.

What is the impact factor of Open Science?
For a publication in an unjournal such as Open Science the question should be: what is the impact factor of my article in Open Science?  During the 2 months review process each reviewer gives the paper a score between 5 (good) and 0 (bad).  This score can be adjusted by the reviewers based on the changes you make within the first 2 months, after that it is fixed. The initial score for your paper is the average of all reviewers final scores.  

If the paper is cited it receives an additional score (called the current score).  The score is determined by the number of citations, and if the citing paper is published in Open Science, the score is weighted by the initial and current score of that paper.  The authors of that paper can also choose to indicate how important your paper was to theirs.  If high scoring papers cite your paper in a positive manner, the current score of your paper increases. Self-citations are not included.  

Why should I review for Open Science?
The work you put into reviewing is now documented for all to see.  Have you contributed greatly to science by identifying Open Science papers with high current scores?  Do the reviews you submit carry more weight with the author and other reviewers as a result?  Some sites now list Open Science reviewers with particularly high impact as a kind of editorial board for the journal.

How should I cite an Open Science paper?
One suggestion is: Author(s), Title, Open Science, date of submission, initial/current score.  If you publish in Open Science using the suggested template, the current score is updated automatically. 

Why should I publish in Open Science?
There are many reasons:
(1) You retain the copyright and anyone can see the paper.
(2) Your paper is accessible upon submission. (Don't rush to publish though: you only have 2 months to get a good initial score).
(3) The impact of your paper is evident in the citation, but disconnected from the conventional impact factor of the journal you managed to get it in to.  The initial score of your paper can help the paper off to a good start, but your truly important papers will ultimately be identified by its current score.
(4) You choose the publishing format you like.  What's your pleasure? machine readable? interactive figures? link to raw data?
(5) Your paper is a living document: comments or questions continue to roll in on important papers and you can update links to your papers (related articles, a new data format) as you see fit.
(6) If you write a good paper, you will get more reviews (i.e. more suggestions and input) but the rantings of a single idiot reviewer will not prevent publication.  Isn't this the place to publish daring and ground-breaking work?  

So what brought this on?
The blogosphere: Egon Willighagen's latest post got me thinking about this particular idea, but the general problems it is trying to address was brought to my attention by many other blogs such as Michael Nielsen's The Future of Science and Is Scientific Publishing About to be Disrupted? posts; most posts by Peter Murray-Rust; Henry Rzepa's long fight to include interactive figures in conventional journals; Mat Todd's excitement for an unconference and the discussion it generated at Derek Lowe's blog.  Why can't we have this in a journal?

Is the Open Science unjournal a good idea?
The blogosphere will decide: no comments on, and no re-blogging of, this post will mean this idea dies a quiet death (by receiving an initial and current score of 0).  But if you get enough smart people fired up about an important idea that can be solved by IT, good things can happen.

iPad: even 3-D molecules that can be viewed from any angle

I recently came across this report on inkling.com, a new company aimed at bringing interactive textbooks to the iPad.  Interactive molecular models was mentioned two times and clearly left an impression on the author (italics are mine):

"Inkling’s software turns textbooks into interactive content, with video, hyperlinks between text and images, notes that can be shared between students and teachers, and even 3-D molecules that can be viewed from any angle."

"MacInnis – who worked at Apple for eight years, including a stint in the company’s educational division — says that the iPad is the perfect device for the kind of interactivity that Inkling provides because it has the ability to produce high-end graphics, such as the 3-D spinning molecule that is a feature of the company’s biology textbook."

This feature is also shown in inklings promotion video, excerpt below:
Update: MacInChemBlog keeps a list of science related iPhone/iPad apps.

Fold.it - Solve puzzles for science

I just came across this amazing game/puzzle/software - call it what you will - Foldit.

It's an interactive protein folder that evaluates the energy on the fly to let you know how well you are doing.

But, and here is the important bit, the energy function is the same used in the Rosetta packages - a state-of-the-art protein folder (at least that's how I read it - the details are a bit sketchy). This is not a toy, but an exciting experiment to test whether human intuition and pattern recognition can compete with Monte Carlo sampling.

The screencast below (see a bigger version here) shows 6 intro puzzles that teaches you some of the techniques for protein folding. You get the program here and make an account for yourself here (making an account using Foldit did not work for me).

When you start Foldit the first time it takes you into the intro puzzles immediately (i.e. bypassing the menu).

I don't know where to start about the many implications of this program for fundamental science, teaching, and public outreach. So I'll simply say wow!, and go on to level 2-3. Not a moment to lose, CASP9 is underway you know!



June 20th, 2010 update:

Not sure why I didn't think to check youtube immediately but there are many videos about foldit. Here are a couple:

Rotating molecules in PowerPoint

Long-time MolModBasics reader/commenter NUChem posted the following question:

"One thing that I've been wondering for a while is creating movie files of optimized structures for presentations. Would it be possible for you to have a screen cast of how to take an optimized structure of cyclohexane and make a movie of the molecule rotating. Basically I have a few polycyclic molecules that I've optimized and I want to be able to have them rotating in my powerpoint presentation so my audience can see the whole molecule. Is there anyway to do this?"

I know of two ways of doing this that are relatively easy. One is to create an animated gif file using the Polyview3D web server, and inserting the file as a movie in Powerpoint. Here is a screencast of how to do this.

Another option is to set the molecule spinning in, for example, Avogadro and then simply record part of the screen using a screencasting program. Unfortunately, it looks as though you have to buy software to do this. There is a free screencasting program called Jing, but you can only save the movie file in the .swf file format, which Powerpoint can't read (and I haven't been able to find a free .swf to .mpeg converter). However, with JingPro ($15/year) you can save the file in the .mpeg format, which should work with Powerpoint, but I haven't tried it myself. I use ScreenFlow ($99) and really like it, but that only works on Macs.

UPDATE: Screencast-o-matic is free, and can make mp4 files, which can be included in Powerpoint.  See this new post for more information.

Of course, with the screencast option you can add animations to Powerpoint of anything, such as vibrations, IRCs, etc. in addition to rotation. However, for more complicated animations I usually switch between Powerpoint and Jmol (more precisely a browser showing an html file with Jmol embedded) during the presentation, ever since I found out I don't have to quit the Powerpoint presentation to switch to another program.

The future of scientific publishing is here today

I recently came across this paper on embedding interactive 3D graphics in pdf files. Unfortunately, I couldn't animate the 3D figures, and I wrote the author (Vlad Vasilyev) who kindly wrote back that:

(1) the publisher (Springer) is a bit behind the times so the interactive figures are found in the supplemental material, but

(2) the ACS is more on the ball, as can be seen in this paper (this is the one I use in the screencast), and

(3) he has made a bunch of tutorials on how to create such diagrams on this page.

This page also contains some pdf files with 3D graphics you can play around with if you don't have access to the papers. Be sure to use Adobe Acrobat Reader 9.

Note that it is also possible to include animations such as vibrational motion (NB: 16 MB file)

Very cool! I haven't tried this myself, but you can be sure I will. Unfortunately, it seems that you need a piece of commercial software (Adobe Acrobat 9 Pro Extended) to do this.

On a related note, check you the interactive figure of interactive figures created by fellow blogger Henry Rzepa (please give the page some time to load).

Just one of those links

Every once in a while you come across a web page that really blows your mind. This is one of them. My first reaction was "I have to learn how to do this!", and this is what really got me interested in Jmol. It took a while, but eventually I came up with something a little bit similar (helped in no small part by this excellent tutorials page) and showed it to everyone that came within shouting distance. You can watch it on a separate page or click on the image here.

In a previous post I showed how to get the coordinate file and the html code. However, the set of commands for this animation is too lengthy to include in the html, so I used a separate script file, which can be downloaded here.

The script is kind of long but of most the lines are actually the same commands used over and over again. For example, here is how I go from a spacefilling model of the protein to just the backbone chain:

select protein
spacefill 400; wireframe 0.0; trace
spin on
set echo top center
echo A protein is long chain that is folded| in a certain way
delay 2
spacefill 300; wireframe 0.3; trace; delay 0.2
spacefill 200; wireframe 0.3; trace; delay 0.2
spacefill 100; wireframe 0.3; trace; delay 0.2
spacefill 0.0; wireframe 0.3; trace; delay 1.0
spacefill 0.0; wireframe 0.2; trace; delay 0.2
spacefill 0.0; wireframe 0.1; trace; delay 0.2
spacefill 0.0; wireframe 0.0; trace;
delay 5
spin off

The key command here is "delay x" which stops the script for x seconds and this is what drives the animation forward. x is what you play with (endlessly).

Then there is the "moveto" command which does the cool repositioning.

echo Let's have a closer look at BADX
moveto 1.0 { -109 890 -443 149.21} 245.66 0.0 0.2 {32.302 28.212 29.408} 45.037945 {0.0 0.0 0.0} 42.396088 -68.80987 50.0;

The input to the moveto command looks very intimidating, but can be generated very easily by the "show moveto" command, as I show in this screen cast.



Finally, the subject of the animated presentation is an ongoing research project. Just like in teaching, animation can be used to bring across very complicated and detailed points to the viewer. Imagine explaining the content of this animation in words! I think molecular animation is a powerful, and overlooked, recruiting tool - as long as there is some kind of guiding narration. So you can also find a link to the animation on my research page.

I have also used snippets of the animation in research talks. But there I have broken the animation into segments, and installed buttons so I can control the timing, using html. More about this in a later post.