pymol_scripts/Native-network.py at master · d8vela/pymol_scripts · GitHub

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import pymol
from pymol import cmd

import sys,os


def nat(pdbid,chainid):

	cmd.view('v', 'store');

	object = cmd.get_names()[0]

	cmd.fetch(pdbid)
	cmd.select("design_nat","%s and chain %s"%(object,"B"))
	cmd.select("native_nat","%s and chain %s"%(pdbid,chainid))

	cmd.select("other_nat","%s and not chain %s"%(pdbid,chainid))
	cmd.hide("everything","other")
	cmd.hide('(resn HOH)')

	cmd.super("design_nat","native_nat")

	cmd.select("none")
	cmd.orient(object)

	cmd.system("rm %s.pdb"%(pdbid));

	cmd.view('v', 'recall')

cmd.extend("nat",nat)

def na():

	cmd.view('v', 'store');

	object = cmd.get_names()[0]

	pdbid = object[0:4]
	chainid = object[4:5]

	cmd.fetch(pdbid)
	cmd.select("design_na","%s and chain %s"%(object,"B"))
	cmd.select("native_na","%s and chain %s"%(pdbid,chainid))

	cmd.select("other_na","%s and not chain %s"%(pdbid,chainid))
	cmd.hide("everything","other")
	cmd.hide('(resn HOH)')

	cmd.super("design_na","native_na")

	cmd.select("none")
	cmd.orient(object)

	cmd.system("rm %s.pdb"%(pdbid));

	cmd.view('v', 'recall')

cmd.extend("na",na)