Model Building with Iodines

Open up Coot          **note: All files saved will save to the root directory that Coot was opened with**

Read pdb and mtz files into the program

Adding iodines

• • Go to "Validate" and "Difference Map Peaks"

  • Input "5.00" into r.m.s.d., click "Find Peaks"          **note: You'll find with Coot that windows that you need will open up behind other programs, so go searching for them**

  • Look for values up to 19.00 for iodine

  • To add iodines, go to "Calculate", then "Model/Fit/Refine", and finally "Place Atom at Pointer"

    • Click "Other", type "I", and you will want to add atom to your pdb file

  • Do this for all difference peaks that seem to be iodines (consult Doug to get this intuition)

After adding all your iodines, make sure to save the new coordinates (why are they new? Because you just added iodines to them!)

• • Also, when saving coordinates, uncheck "Save Hydrogens"

Now, refine this data using Refmac5 rigid body refinement and restrained refinement

Written up by John Y. Lee, June 2014