Tag
ChimeraX
Molecular Modeling PyMOL vs VMD vs ChimeraX: Which Should You Learn? Pick your molecular visualization tool by the job it does. Compare PyMOL, VMD and ChimeraX on licence, platforms and scripting before you… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling How to Extract a Single Chain from a PDB File Pull one chain out of a multi-chain structure with PyMOL, ChimeraX, Biopython or the command line, then check it survives pdb2gmx. Start… Dr. Abdul Rajjak Shaikh 13 min read 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