def project(model, resi1_str, resi2_str, resi3_str, \
symQ, syms_for_use, syms_for_del, sym_d=3, \
segis_for_save='all', segis_for_del=''):
all_segis = prepare(model, resi1_str, resi2_str, resi3_str, segis_for_save, segis_for_del)
new_model, segi_count = make_segis(model, resi1, resi2, resi3, all_segis)
cmd.alter(new_model, \
'segi = new_segi(segi, sorted(all_segis))', \
space={'new_segi': new_segi, 'all_segis': all_segis, 'sorted': sorted})
if symQ:
cmd.symexp('{}_sym'.format(model), \
'{}_save'.format(model), \
'({}_save)'.format(model), \
sym_d)
for i in range(len(syms_for_use)):
cmd.alter('{}_sym{}'.format(model, syms_for_use[i]), 'segi=segi+"mod{}"'.format(i + 1))
merge(model, ['{}_save'.format(model)] + ['{}_sym{}'.format(model, s) for s in syms_for_use])
else: merge(model, ['{}_save'.format(model)])
for sym in syms_for_del:
cmd.delete('{}_sym{}'.format(model, sym))
cmd.alter('all', 'chain="A"')
cmd.save('{}_calc.cif'.format(model), '{}_calc'.format(model))
print(cmd.rms_cur('{}_calc'.format(model), '{}_sym'.format(model)))
def testSymexp(self):
cmd.load(self.datafile('1oky.pdb.gz'), 'm1')
n = cmd.count_atoms()
cmd.symexp('s', 'm1', '%m1 & resi 283', 20.0)
x = cmd.get_object_list()
self.assertEqual(x, [
'm1',
's01000000',
's03000000',
's04000000',
])
self.assertEqual(n * 4, cmd.count_atoms())
# Fetch structure
structure = '5FYL'
cmd.reinitialize()
cmd.delete('all')
cmd.fetch(structure) #, type='pdb1')
# Remove non-Env chains
# gp41 = chain B
# gp120 = chain G
# 35O22 = chains D and E
# PGT122 = chains H and L
cmd.remove('c;D,E,H,L,U,V')
# Generate symmetry partners based on crystal structure
cmd.symexp(structure, structure, structure, 3)
# Tweak initial display and color of Env monomers
cmd.hide('everything')
cmd.bg_color('white')
cmd.show('cartoon')
cmd.color('grey40')
#cmd.color('grey20', structure)
cmd.set('cartoon_transparency', '0.5')
cmd.set('cartoon_transparency', '0', structure)
#cmd.hide('hetatm')
# Identify unique sites in structure
sites_in_structure = []
cmd.iterate("(name ca)", "sites_in_structure.append(resi)")
unique_sites_in_structure = []
homologs = ['BG505', 'BF520']
for h in homologs:
# Fetch structure
structure = '5fyl'
cmd.reinitialize()
cmd.delete('all')
cmd.fetch(structure) #, type='pdb1')
# Remove non-Env chains
# gp41 = chain B
# gp120 = chain G
# 35O22 = chains D and E
# PGT122 = chains H and L
cmd.remove('c;D,E,H,L,U,V')
cmd.symexp(structure, structure, structure,
3) # generate symmetry partners based on crystal structure
# Tweak initial display and color of Env monomers
cmd.hide('everything')
cmd.bg_color('white')
cmd.show('cartoon')
cmd.color('grey40')
#cmd.color('grey20', structure)
cmd.set('cartoon_transparency', '0.5')
cmd.set('cartoon_transparency', '0', structure)
#cmd.hide('hetatm')
# Identify unique sites in structure
sites_in_structure = []
cmd.iterate("(name ca)", "sites_in_structure.append(resi)")
unique_sites_in_structure = []
"""
# Imports
import pymol
from pymol import cmd
# Fetch structure
structure = '1ENV'
cmd.reinitialize()
cmd.delete('all')
cmd.fetch(structure) #, type='pdb1')
# Generate symmetry partners based on crystal structure, using a distance of
# 1.9 since this reproduces the timer without segments from any other adjacent
# monomers in the crystal structure
cmd.symexp(structure, structure, structure, 2.5)
# Tweak initial display and color of Env monomers
cmd.hide('everything')
cmd.bg_color('white')
cmd.show('cartoon')
cmd.color('grey40')
#cmd.set('cartoon_transparency', '0.5')
#cmd.set('cartoon_transparency', '0', structure)
# Get site-specific RMSDcorrected values and whether the shift at a site is
# significant
RMSD_dict = {}
sig_dict = {}
with open('../BG505_to_BF520_prefs_dist.csv') as f:
lines = f.readlines()[1:]
"""
# Imports
import pymol
from pymol import cmd
# Fetch structure
structure = '1AIK'
cmd.reinitialize()
cmd.delete('all')
cmd.fetch(structure) #, type='pdb1')
# Generate symmetry partners based on crystal structure, using a distance of
# 1.9 since this reproduces the timer without segments from any other adjacent
# monomers in the crystal structure
cmd.symexp(structure, structure, structure, 1.9)
# Tweak initial display and color of Env monomers
cmd.hide('everything')
cmd.bg_color('white')
cmd.show('cartoon')
cmd.color('grey40')
#cmd.color('grey20', structure)
cmd.set('cartoon_transparency', '0.5')
cmd.set('cartoon_transparency', '0', structure)
#cmd.hide('hetatm')
# Identify unique sites in structure
sites_in_structure = []
cmd.iterate("(name ca)", "sites_in_structure.append(resi)")
unique_sites_in_structure = []