Hello, I'm taking an undergrad bioinformatics class and we have to identify salt bridges in a specific nucleosome structure (mine is 3WKJ) given to us (from the protein database/pdb file). The class has been given info that: Phosphorus atom has -1 charge, a positive charge lies on NZ atom of LYS and a positive charge lies on NH2 atom of ARG. My professor wants us to find salt bridge interactions less than 7 angstroms. MY TA specified that we need to show "salt bridge interactions/clusters between [ARG, LYS] and the [A, T, G, C]." I've searched the web but I'm unsure how to identify these salt bridges on pymol. It would be great if someone could help me in solving this problem. Thanks.
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What your professor wants is for you to find all phosphorous atoms within a specific range (0-7Å) of an NZ or NH2 atoms of a Lys or Arg residue. Have a look at the Pymol wiki, namely the selection syntax and macros (e.g. within, around, byres, etc), an iterate. This should put you on your path to get a comprehensive list of salt bridges with Pymol.
Without any other information, specifically on your background, there's not much else to say.
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João Rodrigues
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This looks like an interesting assignment. You will definitely feel like you've accomplished quite a bit and learned PyMOL queries once you get this done. This might be a good primer for you to begin: http://pymol.sourceforge.net/newman/user/S0220commands.html