#!/bin/bash

$ROSETTA3/source/bin/rosetta_scripts.linuxgccrelease \
	-in::file::s starting_single_dimer.pdb \
	-parser::protocol asymm_refine.xml \
	-parser::script_vars denswt=35 rms=1.5 reso=4.4 map=TetraAllPF_8nm_half1_b250_f4_4A_corr.mrc testmap=TetraAllPF_8nm_half2_b250_f4_4A_corr.mrc\
	-ignore_unrecognized_res \
	-edensity::mapreso 4.4 \
	-default_max_cycles 200 \
	-edensity::cryoem_scatterers \
	-beta \
	-out::suffix _$1\
	-crystal_refine
	-extra_res_cen GTP.cen.params GDP.cen.params 
	-extra_res_fa GTP.fa.params GDP.fa.params
	-extra_improper_file GTP.fa.tors GDP.fa.tors