pymol

generate dimer from a monomer

  • fetch 4ryl
  • symexp 4ryl, 4ryl, 4ryl, 3
references and materials:
  1. protein structure - Generate full dimer from monomer with C2 symmetry? - Biology Stack Exchange
  2. How can I generate a dimer from a given conformation of a monomer, without any information from a crystal structure? | Schrödinger (schrodinger.com)

select

  • select resn ARG and name NH1 or name NH2
  • select resn GLU and name OE1 or name OE2
  • dist 1, ARG_N, GLU_O, 5, mode=2
references and materials:
  1. Selection Algebra - PyMOLWiki
  2. Distance - PyMOLWiki

for-loop

  • PyMOL>for i in [1,2,3]: cmd.group("%s-com"%(i), "%s*"%(i))