PHYC500/2007:Supporting material: Difference between revisions

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*Thanks to those who came for my talk!  Here's my slides if you want to take a look:  [[Media:Phys500_pikaart.pdf]]
*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 [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 computation 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.

Revision as of 09:38, 2 February 2007

Steve Koch talk, January 18

Mike Pikaart talk, February 1

  • 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.