Watoc luca-de-vico-21-july-2011
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Friday, July 29, 2011
Thursday, July 28, 2011
Sunday, July 24, 2011
Jan's talk at WATOC 2011 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
Thursday, July 21, 2011
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.
New paper: Ring current effects in proteins
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 (ΔδRC) 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 ΔδRC 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 ΔδRC 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 ring current effect on chemical shifts of amide protons (ΔδRC) 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 ΔδRC 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 ΔδRC 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.
Tuesday, July 19, 2011
Sunday, July 17, 2011
Thursday, July 14, 2011
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