1. What were my goals for this week?
- Literature search for TLS
- Literature search for motion segmentation and clustering
- Get comfortable with VMD and PiMol
- Get PDBs for 3ANK and Adenylate kinase
- Go over what people are looking for when they look at motions
2. What did I accomplish this week?
- Extensive reading of TLS articles
- Work through user manual for VMD
- Found PDBs for 3ANK and Adenylate kinase - need to speak with Aaron re: 3ANK with motion
- Found references in papers to purposes of motions
- Got Ono's website live
- Spoke with Julie Mitchell regarding future web dev for mitchell-lab -- only when Gleicher's gone
3. Why are numbers 1 and 2 different?
Ono and Mitchell were fairly last-minute set-ups, but didn't significantly conflict with work here. Didn't have to do literature search for TLS, since Gleicher's initial search turned up extensive material that took longer than expected to work through (mathy). Because of that, didn't have time to do lit search for motion segmentation and clustering; moving that to next week. Also didn't have time to find PiMol and familiarize myself with it, also moving that to next week.
Also, wallace gave me tons of problems. I need to pick a new machine.
4. What are my goals for next week?
- Literature search for motion segmentation and clustering
- Get comfortable with PiMol
- Go through a Python tutorial
- Start playing around with some two-dimensional analogues from Gleicher, generate some images
- Speak to Aaron re: 3ANK with motion
5. How does this fit in my bigger picture?
More foundational material, definitely found some things (using TLS) to help with the segmentation of the protein for determining gross overall movements. Hope to do some basic combination of TLS and NMA techniques to find some good visualizations.
6. What did I read this week?
- Painter, Jay and Ethan A. Merritt, A molecular viewer for the analysis of TLS rigid-body motion in macromolecules
- Cruickshank, D.W.J., The analysis of the anisotropic thermal motion of molecules in crystals
- Lin, Shuo Liang et al, Molecular surface representations by sparse critical points
- Karney, Charles F.F., Quaternions in molecular modeling
- Schomaker, Verner and K.N. Trueblood, On the rigid-body motion of molecules in crystals
- Painter, Jay and Ethan A. Merritt, TLSMD web server for the generation of multi-group TLS models
- Frauenfelder, Hans, New looks at protein motions
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