Files and tips for analysis of diffraction data and electron density maps
| Diffraction |
Diffraction data for determination of unit cell parameters |
chem112.mtz |
| Structure |
Amino acids for structure fitting for PyMol |
chem112.pdb |
| Structure |
Startup file with amino acids for O |
chem112.o |
| Structure |
Electron density map for O or PyMol |
chem112.omap |
Students in the class use "O" to perform the fitting. However, it appears that this excercise can be accomplished also with PyMOL. Here are a few tips on how to get started:
- Read in the PDB file with amino acids via File ... Open ...
- Read in the density map via File ... Open ...
- Create isomesh object: isomesh msh0, chem112, 1.2, (resid 356:365), 0.0, 0
- Color isomesh: color lime, msh0
- Emphasize residue to be fitted: show sticks, resn glu
- Pick Glu residue with mouse
- Use mouse controls (see mouse key box) to move and rotate selected residue
- If things go wrong, you can undo changes via Ctrl-Z
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