The “name” means atom names, e.g. n for nitrogen (backbone), yes, you would use “name” (or n. in short) in your command.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Alex Lee Sent: Friday, March 17, 2017 2:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb] Pymol alignment command grammar help Dear CCP4BB members, I tried to use pymol command to align two proteins, I read the pymol wiki and I could not understand the command grammars (I am not computer major and not familiar with machine language). For example pymol wiki says as below: Furthermore, you may wish to restrict the alignment to just the backbone atoms, so you can say: align structure2 and resi 1-100 and name n+ca+c+o, structure1 and resi 300-400 and name n+ca+c+o or in short form: align structure2 & i. 1-100 & n. n+ca+c+o, structure1 & i. 300-400 & n. n+ca+c+o My questions are: 1. what does "name" mean in the command, should I just type "name" as is in the pymol command? 2. If I want to align two conserved helix of a protein dimer (each helix is on one monomer) to its single point mutant (mutation is not in the conserved helix region), as the helix is on different protein chains, could I write one command as: align structure 2 and chain X and resi xxx and chain Y and resi xxx and name ca, structure 1 and chain X and resi xxx and chain Y and resi xxx and name ca? Thanks for any input on this.
