PHYC500/2007:Supporting material: Difference between revisions
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*If you are interested in ways to look at protein structures, go to [http://www.rcsb.org the PDB website]. PDB is the "Protein Data Bank," i.e. the repository for just about all known biomolecule structures. You can find structures in the "Site Search" window either by entering the unique PDB ID if you know it for the structure you're looking for - for example, 2GAT is the structure of the Gata-DNA complex - or by name. Entering "2GAT" will pull up the structure with a little cartoon of it on the righthand side. Underneath the cartoon (where it says "Display Options") you can open the structure in various viewers. The simpler ones open right up as Java applications, so KiNG (the most esthetically enjoyable of them in my opinion), Jmol (which looks a lot like Chime), and Webmol (Rasmol-esque). The Swiss-pdb viewer is a lot like the PyMol viewer I showed (available [http://pymol.sourceforge.net/ here]); that's a plugin you install on your machine. In the not-for-the-faint-of-heart category, the big daddy of them all is the program [http://www.ks.uiuc.edu/Research/vmd/ VMD] (Visual Molecular Dynamics) from UIUC, which is a great way to tie into computational chemistry approaches. | *If you are interested in ways to look at protein structures, go to [http://www.rcsb.org the PDB website]. PDB is the "Protein Data Bank," i.e. the repository for just about all known biomolecule structures. You can find structures in the "Site Search" window either by entering the unique PDB ID if you know it for the structure you're looking for - for example, 2GAT is the structure of the Gata-DNA complex - or by name. Entering "2GAT" will pull up the structure with a little cartoon of it on the righthand side. Underneath the cartoon (where it says "Display Options") you can open the structure in various viewers. The simpler ones open right up as Java applications, so KiNG (the most esthetically enjoyable of them in my opinion), Jmol (which looks a lot like Chime), and Webmol (Rasmol-esque). The Swiss-pdb viewer is a lot like the PyMol viewer I showed (available [http://pymol.sourceforge.net/ here]); that's a plugin you install on your machine. In the not-for-the-faint-of-heart category, the big daddy of them all is the program [http://www.ks.uiuc.edu/Research/vmd/ VMD] (Visual Molecular Dynamics) from UIUC, which is a great way to tie into computational chemistry approaches. | ||
==Keith Lidke talk, February 15== | |||
Some background material: | |||
A wonderful website with a tremendous amount of information about microscopy including fluorescence microscopy: | |||
[http://microscopy.fsu.edu/primer/techniques/fluorescence/fluorhome.html microscopy.fsu.edu] | |||
A link to our Optics Express paper demonstrating super-resolved blinking quantum dots: | |||
[http://oe.osa.org/abstract.cfm?id=85379 Superresolution by localization of quantum dots using blinking statistics] | |||
</div> | </div> | ||
Revision as of 14:37, 14 February 2007
Steve Koch talk, January 18
- Here is a 10 MB file of his slides: Media:070117 PHYC 500 Koch Presentation.ppt (It's a powerpoint file, not MS Word...you can find the file on the course website too.) Videos from the talk (I didn't show these, so they probably won't make sense, but putting on because slides link to them):
- No Force Epi
- 700 fN Epi
- Evanescent Wave Detection, Cycling force off / on
Mike Pikaart talk, February 1
- Thanks to those who came for my talk! Here's my slides if you want to take a look: Media:Phys500_pikaart.pdf
- If you are interested in ways to look at protein structures, go to the PDB website. PDB is the "Protein Data Bank," i.e. the repository for just about all known biomolecule structures. You can find structures in the "Site Search" window either by entering the unique PDB ID if you know it for the structure you're looking for - for example, 2GAT is the structure of the Gata-DNA complex - or by name. Entering "2GAT" will pull up the structure with a little cartoon of it on the righthand side. Underneath the cartoon (where it says "Display Options") you can open the structure in various viewers. The simpler ones open right up as Java applications, so KiNG (the most esthetically enjoyable of them in my opinion), Jmol (which looks a lot like Chime), and Webmol (Rasmol-esque). The Swiss-pdb viewer is a lot like the PyMol viewer I showed (available here); that's a plugin you install on your machine. In the not-for-the-faint-of-heart category, the big daddy of them all is the program VMD (Visual Molecular Dynamics) from UIUC, which is a great way to tie into computational chemistry approaches.
Keith Lidke talk, February 15
Some background material: A wonderful website with a tremendous amount of information about microscopy including fluorescence microscopy: microscopy.fsu.edu A link to our Optics Express paper demonstrating super-resolved blinking quantum dots: Superresolution by localization of quantum dots using blinking statistics
