IGEM:MIT/2006/MichaelsSNoteBook/2008-3-12

Wednesday, 03/12/08
Jay, my personal online wiki notebook :).

I think this that this is the most appropriate way to handle my thoughts and write down what I did during the day.

Sooo lets get startet.

After my issues with the new wLAN Box in the lan, I computed the PROCHECK (all dihedral) and MolProbity z-scores via PSVS in all my structure pairs. As expected, the NMR structures have significantly lower z-scores than the corresponding high-res X-ray structures. Keep in mind, that the Z-scores are calibrated with high res X-rays.

I should read the paper one more time before I try to interpret them, but so far the result is not really suprising, since most of my structure pairs have poorer performance in my design calculations.

Also, I deal't the issues with 1KF5_2AAS, seems there were some inconsistensies with my X-ray structure ... What the hell is acually a ANISOU entry ? And there were SEVERAL alternate coordinates for GLN, ASN and SER residues. I've just chosen to keep the "A" alternate coordinates for each residue, hopefully the structure behaves know like it should.

And I should start to write the Methods section of the paper -_-.