[phenixbb] viewing ligand_identification output files

Emilia C. Arturo (Emily) eca38 at drexel.edu
Sat Mar 14 10:54:50 PDT 2015


I've recently used--for the first time--phenix's ligand_identification
tool via the GUI, and am now examining the output files. I'm writing
to ask for advice on how to view the map and models using Coot. I
could open the 'model_RSR_FITTED_###.pdb' file with PyMOL, and I could
inspect where in the model the fit ligand sits, but I prefer to look
at the map using Coot. At this point I have two problems:

First, when I Auto Open the resolve.mtz file in Coot, the model I'd
input to ligand_identification is clearly not aligned with the map.
What could have happened here? And how might I fix it?

Second, the same 'model_RSR_FITTED_###.pdb' file I opened with PyMOL
has in Coot just one chain, and that contains only the fit ligand.

Thanks in advance for any input,

Emily Arturo
Ph.D. program in Biochemistry, Drexel Univ College of Medicine
Jaffe lab, Fox Chase Cancer Center
Philadelphia, PA

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