Hi guys,
Using the PDB NGL viewer, I can see there is a ligand (such as a drug inhibitor) binding to a pocket of my interest protein. But when i download this PDB file and visualize it with VMD, the ligand is missing. I am new to protein structure database, so any suggestion would be great!
Thanks in advance!
Serdar Durdagi
most likely, you are trying to visualize the structure with cartoon, etc. drawing style in drawing methods in VMD; thus you can't see the ligand; try "lines" or "licorice" as drawing method
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Ramin Ekhteiari Salmas
Before using any software, I strongly recommend you to read its manual.
Both you and VMD are from University of Illinois.
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