Sunday, August 26, 2012

Funny code comments

Funny code comments is a perennial topic of conversation over group lunch. This one was found by Casper, in the Fock2 subroutine.  It's part of the MOPAC6 six code I implemented in GAMESS back in 1992, but I didn't add it.  Perhaps Mr MOPAC?


Have you come across funny code comment?

Wednesday, August 22, 2012

Writing grant proposals versus working in industry

It seems like I am always working on a grant proposal - or a pre-proposal, which is a proposal that gives the successful applicant permission to write and submit an even longer proposal.

Recently, one call to the European Science Foundation required you to submit both the pre-proposal and the full proposal simultaneously! That call got over 700 applicants and 4% went on to the second round.  Mine wasn't one of then.

It is times like this when the grass looks greener in industry, but as the following documentary reenactment comedy sketch seems to indicate it's not all milk and honey there either.

Monday, August 20, 2012

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:
- 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!

- 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...

Thursday, August 16, 2012

Publishing in PLoS ONE

After having gotten two papers accepted with PLoS ONE, the most surprising thing that you get for your $1350 USD has nothing to do with the quality of a review you get back, the style of publication or the number of pages you write. No. what you get is enormous amounts of work regarding your manuscript about files, formats, what you can't, shan't and what the production staff won't touch unless you 'fix' issues that they could have done easily. However, the most annoying thing is that each time there is a new issue/interaction you get to have a new person. Furthermore, as you get new production-staff all the time, their rules change. For instance, I got this email this morning:
For references, PLoS uses the numbered citation (citation-sequence) method. References should be cited in numerical order on first mention in the text. Citations should be indicated by the reference number in square brackets. See refs 21 and 42
which I understand. However, the production staff on the EFMO paper fixed this without notifying me (something you might would expect for the $1350 you pay up front).

Second of all, every email ends with

We apologize if any of these items were not requested previously. We sincerely appreciate your efforts to help us format your manuscript for publication.
so after three different persons from the PLoS Production Staff I get three different emails with different issues and different rules, but they all end with that line which got me to write this post in the first place.

Here is my short list of things that I have to remember for next time I'll upload an MS to PLoS ONE

  • Even though you can upload supporting information in zip-files during the review, the published paper cannot include zip-files. So you 20 example files will have to be uploaded separately each with their own little legend (like I got nothing else to do?)
  • Images should not be provided in EPS format. Take the time yourself to make the TIFF image right away since PLoS ONE apparently does what their guidelines state which can also be unsatisfying (upscale PDF, take screenshot, save TIFF)
  • The above point is especially important if you have line-figures or chemical reactions. Most programs will have some crazy setup when saving to whatever native format which looks good on screen, but you have to be sure that your TIFF is 300 dpi (even though most people read the web-version anyways and they use a downscaled image for that)
  • The provided Latex template (bibtex style file actually) cannot format a citation correctly according to what they recommend (see here for instance). The staff has been notified of this and some Latex-wizzard is apparently on the case. Until then. Have fun citing PLoS ONE papers in a PLoS ONE publication.

Oh well, that was a minor rant. I still love you PLoS ONE.

Thursday, August 9, 2012

One Way To Center a Molecule from a Gromacs calculation

When you run an MD the molecule or ligand of interest might drift a little inside your box. Sometimes (oftentimes?) you want to center that ligand and force it to be there always. Searching the internet gave me inspiration but no solution. So thinking of a solution (and reading the manual a little more carefully) I ended up figuring out that one needs to run the trjconv tool multiple times to achieve proper results. It is only specified indirectly in some of the manuals and help-documents I've been able to find.

Here is a script that will ask you what you want to center (be sure that it has a proper index in the topology file).

Happy centering.

Wednesday, August 8, 2012

Second PLoS ONE article accepted!

Casper's second paper "FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations" has been accepted on August 8th just 6 days after resubmitting it a lengthy response. It was originally submitted on May 22nd.

If you can't wait to read the paper, it has been available on arXiv the entire time.

FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

Dear Mr Steinmann,

I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE.

Your manuscript will now be passed on to our Production staff, who will check your files for correct formatting and completeness. After this review, they may return your manuscript to you so that you can make necessary alterations and upload a final version.

Before uploading, you should check the PDF of your manuscript very closely. THERE IS NO AUTHOR PROOFING. You should therefore consider the corrected files you upload now as equivalent to a production proof. The text you supply at this point will be faithfully represented in your published manuscript exactly as you supply it. This is your last opportunity to correct any errors that are present in your manuscript files.

If you or your institution will be preparing press materials for this manuscript, you must inform our press team in advance. Please contact them at

If you have any questions, concerns, or problems, please contact us at, and thank you for submitting your work to our journal.

With kind regards,
Academic Editor

Monday, August 6, 2012

Revised version of BioFET-SIM Web Interface: Implementation and Two Applications

A revised version of "BioFET-SIM Web Interface: Implementation and Two Applications" (Martin's second PLoS ONE paper) has been re-submitted to PLoS ONE and deposited at arXiv.

Our comments to the reviewers are summarized here.

In the process the web interface was significantly improved and Martin's has made some new screencasts:

Thursday, August 2, 2012

Revised version of Casper's second PLoS ONE paper

The answers to the review of Casper's second PLoS ONE submission on the FragIt tool have been submitted. An updated manuscript have been submitted to It is to be published Friday August 3rd, but stay tuned here for info on when it is available or h Have fun testing out your own proteins on the FragIt homepage in the meantime.

FragIt 1.0.1 is available for download.

update: the paper is now available at (August 3rd, 2012)