[Jmol-users] How does Jmol know the \alpha-helix and \beta-sheet

Dear Jmol developers and users, I am always thinking about the question that how does Jmol display the secondary structures of proteins. As we know, the secondary structures are related to the hydrogen bonds between the C=O and H-N groups of the amino acid residues. However, in many of the PDB fi

[Jmol-users] Running Jmol in Linux command line

Dear Jmol developers and users, I am a newbie to Jmol and I have a question on running Jmol in Linux command line. Previously, when I prepared Ramachandran plot, I used Jmol interface to open PDB file and typed command in Jmol console as: *write ramachandran "OUTPUT_FILE_NAME"* That was very low