PyMOL on the iPad

I just got an email (labeled as spam for who knows reason) from Schrödinger saying that they made PyMol available for the iPad, and most of all for free. Now, who am I to resist and not try it head on? In fact I downloaded it immediately.

First impression: very negative! It starts with a very condensed help panel, closing which one should see a demonstration molecule. The molecule did not show up because the app says that I have not enough free memory on my device! So, here we have me with big expectations staring at a black screen with just a couple of buttons on the top. So sad.

Never mind, I decided to try and load another protein structure from the pdb. Second impression: amazing! One can finally "touch" proteins, rotate and move and zoom them as one wishes. There are the familiar ways of displaying a structure (e.g. lines, cartoon etc., but not ball-and-sticks for non ligands) and many possibilities for performing a selection. It is only 10 minutes that I'm playing with it, so I haven't figured out all the available tools. One thing I tried is to ray trace (yes, ray tracing!) the actual scene I had. The app miserably crashed.
My guess is that the app could become a nice tools for both (self-)education and production of nice images.

Here is my good-bad list after 10 minutes of playing around:
good
- possibility to load structures from many different sources (pdb, dropbox and others)
- possibility for different rendering
- possibility to directly save screenshots
- multiple structures can be displayed
- but most of all you can rotate them with your finger tips!

bad
- it seems it requires a lot of memory
- no possibility (at least I haven't found out) to fade out parts of the structure other than that one is interested in

One more thing: it would be soooooo great if Schrödinger would distribute the code behind the structure visualizer. It would open up many possibilities for visualizing a structure inside another app. Think like BioFET-SIM 2.0 on the iPad...

The scientific tax return

Every year I, and other permanent research staff at the Faculty of Sciences, must fill out a "scientific tax return" (the Faculty's name for that, no mine), which is an online form with a bunch of questions.

I have included the questions related to publications below.   Without going into whether such a survey is a good idea at all, there are some messages that this survey sends (assuming one worries about this at all):

1. Don't publish in new journals (they have an impact factor of 0).
2. Don't publish in journals that are not indexed on the Web of Science (they don't contribute to your citations and have an impact factor of 0).
3. Blog posts don't count (I have written 7 blog posts that each were viewed more than 1000 times in the last 12 months)
4. Software doesn't count (for example the PROPKA webserver has been accessed 20,609 in the last 12 months)

Now that we have this thing called the internet, scientific communication and impact, has become so much more than conventional journal articles.

On a positive note, I do like that they ask many different questions, because that gives a better picture about productivity than a single number.

Questions Related to Publications
* Total number of peer reviewed publications published in 2010 (please do not include publications that were still "in press" by the end of 2010)

* Total number of peer reviewed publications published in 2010 included in Web of Science. See manual below.

* Total number of monographs published in 2010 (please do not include publications that were still "in press" by the end of 2010)

* Sum of Journal Impact Factors of all publications published in 2010, see for this table for present JIFs and WikiPedia for more information.

* Number of citations in 2006-2011 for publications from the period 2006-2010, including both years. See manual below.

* Total number of citations for your entire academic career. See manual below.

* Total number of publications from 2006-2010, including both years.

* Hirsch-Index. Hirsch-Index for your entire professional career (XXXX-2011). See WikiPedia and instructions below.

The form had a comments section.  Here is what I wrote.
Publication/Scientific Communication:
* I published the book Molecular Modeling Basics, which has sold 461 copies in 2010.
* I continued to run the blog molecularmodelingbasics.blogspot.com, which received 37,700 visits in the last 12 months.

Journalist: force scientists to blog

A journalist from Berlingske (a major Danish newspaper) has, on his own blog (in Danish, sorry!), suggested that researchers should be forced to blog.  Be sure to read the comments.

Here's one response from another blogger (also in Danish, sorry!). 

My first attempt at e-publishing

I have made an electronic color supplement to my book.  Read more on Molecular Modeling Basics

Smelling vibrations: why do isotopomers have different smells?

An interesting paper (I assume, I haven't read it yet) led to an interesting blog post (I did read that one) with an interesting discussion (be sure to check out the comments below, including those of the paper's author). 

Science in action and science in the open.

Visualized molecules can make chemistry comprehensible

From the Departmental news letter written by Jes Andersen:

When students experience chemistry as “tough stuff”, it’s often due to the difficulty of fully appreciating molecules that are too small and reactions that are too fast. Chemistry professor Jan Jensen has a method of making chemistry much more visible. Using computer-based simulations and visualisations, he offers his students a more intuitive and less abstract gateway into the field of chemistry. Now, Jensen and his colleagues at the Centre for Computational Molecular Science have received 200,000 kroner from the University’s “Education at its Best” project to develop and diffuse visualisation tools throughout the courses of his fellow chemistry instructors. He is convinced that these tools will make it a bit easier to become a chemist.

“In the oral examinations, I’ve noticed that even those who are quite poor at equations have improved in their ability to explain what is going on at the molecular level,” explains Jensen. In the coming months Jensen and his collaborators in the Centre for Computational Molecular Science will adapt the visualisation tools to courses at the University of Copenhagen.

The hope is that ambassadors from the Centre will ensure that the visualisation methods spread like ripples across water. While Jensen expects to employ student interns to create finished “instruction packages”, he encourages curious professors to sign up for the development phase. “I am confident that this will make it easier to teach chemistry. But here at the beginning, it would be more fun to test ideas in collaboration with professors who actually have a desire to use these tools,” affirms Jensen who is confident that these methods will benefit instructors as well. “I have a few lectures where I do not use the visualisations and I can clearly see that I lose the students’ attention,” concludes Jensen.

Read Jan Jensen’s blog post about visualisation.
Read about the grant.

Three chemistry bloggers on why you should blog

Noel O'Boyle: Don't keep your cool - share it

Henry Rzepa: Is there a difference between a scientific blog and scientific journal?

Steven Bachrach: Why blog?

Skillful writing of an awful research paper

by Royce Murray

Rule 1.
Never explain the objectives of the paper in a single sentence or paragraph and in particular never at the beginning of the paper.

For the rest of the rules click here.