[phenixbb] viewing ligand_identification output files

Li-Wei Hung lwhung at lbl.gov
Sat Mar 14 14:29:09 PDT 2015

Dear Emily,

Sorry for the problem.  I just tested two test runs and the 
ligand_identification gui appeared to behave properly.
On the 'Results' page, choose the ligand you want to view from the list, 
click on the 'open in Coot'  button on the lower left corner, a Coot 
window should show up with the ligand, difference map, and protein (if 
included in the run) all arranged nicely. You don't need to specify the 
map or pdb files in Coot to display the results.  If this is what you 
did, and it still show the problems you described, could you send me you 
input files off list so I can pinpoint the problems.

Thank you,


Emilia C. Arturo (Emily) wrote:
> Hello,
> 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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