Tag
ChimeraX
Molecular Modeling How to Remove Water Molecules From a PDB File for Docking Strip HOH waters and crystallisation additives from a PDB file with PyMOL, ChimeraX or pdb-tools, and learn which structural waters to keep. Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Fix Missing Residues and Loops in a PDB Structure Before Docking or MD (ChimeraX, SWISS-MODEL and MODELLER) Find the gaps your crystal structure never resolved, decide which ones matter, and rebuild them in ChimeraX, SWISS-MODEL or MODELLER before docking… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling UCSF ChimeraX Tutorial for Beginners: Load, Inspect and Clean a Protein Structure Learn UCSF ChimeraX in one sitting: fetch a PDB entry, master the 12 core commands, then clean the structure for docking or… Dr. Abdul Rajjak Shaikh 13 min read Updated