def run_script(session):
from chimerax.atomic import selected_residues
from chimerax.build_structure import modify_atom
from chimerax.build_structure.mod import ParamError
from chimerax.core.errors import UserError
sel = selected_residues(session)
if len(sel) != 1 or sel[0].name not in ('ASP', 'GLU'):
raise UserError('Please select a single ASP or GLU residue!')
sel = sel[0]
if sel.name == 'ASP':
pos = 'D'
else:
pos = 'E'
o_atom = sel.find_atom(f'O{pos}2')
other_o = sel.find_atom(f'O{pos}1')
if o_atom is None or other_o is None:
raise UserError(
'Selected acid sidechain is missing one or both of its oxygen atoms!'
)
if len(o_atom.neighbors) != 1 or len(other_o.neighbors) != 1:
raise UserError(
'Selected acid sidechain already has a substituent on its carboxyl group!'
)
new_h = modify_atom(o_atom,
o_atom.element,
2,
connect_back=False,
res_name=sel.name)[1]
new_h.color = [255, 255, 255, 255]
def _sel_res_type(self):
from chimerax.atomic import selected_residues
sel_residues = selected_residues(self.session)
sel_res_types = set([r.name for r in sel_residues])
if len(sel_res_types) == 1:
return self.rot_lib.map_res_name(sel_res_types.pop(),
exemplar=sel_residues[0])
return None
def run_script(session):
from chimerax.atomic import selected_residues
models = selected_residues(session).unique_structures
for m in models:
atoms_with_alt_locs = m.atoms[m.atoms.num_alt_locs > 0]
m.delete_alt_locs()
atoms_with_alt_locs.occupancies = 1
session.logger.info(
('Removed all altlocs in #{}.'
'Occupancies for all affected atoms have been reset to 1.').format(
', '.join(m.id_string for m in models)))
def run_script(session):
from chimerax.atomic import selected_residues
from chimerax.isolde.atomic.building.build_utils import create_disulfide
sel = selected_residues(session)
if len(sel) != 2 or not all(sel.names == 'CYS'):
from chimerax.core.errors import UserError
raise UserError('Please select two cysteine residues!')
if sel[0] not in sel[1].neighbors:
create_disulfide(*sel)
session.logger.info('Created disulphide bond between {}.'.format(
' and '.join([
'{}{}{}'.format(c.chain_id, c.number, c.insertion_code)
for c in sel
])))
def run_script(session):
sel = selected_residues(session)
if not len(sel):
raise UserError('No atoms selected!')
sel = sel[sel.polymer_types == Residue.PT_AMINO]
if not len(sel):
raise UserError('No protein selected!')
us = sel.unique_structures
if len(us) != 1:
raise UserError('Selection must be from a single model!')
m = sel.unique_structures
cids = sel.unique_chain_ids
for cid in cids:
chain = m.chains[m.chains.chain_ids == cid][0]
last_res = chain.residues[-1]
add_oxt(session, last_res)
def run_script(session):
from chimerax.atomic import selected_residues, selected_bonds, Residues
sel = selected_residues(session)
if len(sel) != 2 or not all(sel.names=='CYS'):
b = selected_bonds(session)
if len(b) == 1:
b = b[0]
sel = Residues([a.residue for a in b.atoms])
if len(sel) != 2 or not all(sel.names=='CYS'):
from chimerax.core.errors import UserError
raise UserError('Please select exactly two cysteine residues!')
from chimerax.isolde.atomic.building.build_utils import break_disulfide
break_disulfide(*sel)
session.logger.info('Broke disulphide bond between {}.'.format(
' and '.join(['{}{}{}'.format(c.chain_id, c.number, c.insertion_code) for c in sel])
))
def run_script(session):
from chimerax.atomic import selected_residues
from chimerax.core.errors import UserError
from chimerax.atomic import next_chain_id
#from chimerax.isolde.atomic.building.merge import merge_fragment
#from chimerax.geometry import Place
session.logger.info('ISOLDE: merge models')
if not hasattr(session, 'isolde'):
raise UserError('ISOLDE must be running')
target = session.isolde.selected_model
if target is None:
raise UserError('ISOLDE has no model initialised!')
selres = selected_residues(session)
us = selres.unique_structures
others = [s for s in us if s != target]
if not len(others):
from chimerax.core.errors import UserError
raise UserError('Must have at least two atomic models selected!')
session.logger.info(
f'Merging models {",".join([f"#{m.id_string}" for m in others])} into #{target.id_string}.'
)
seen_ids = set(target.residues.unique_chain_ids)
for s in others:
chain_id_mapping = {}
chain_ids = sorted(s.residues.unique_chain_ids)
for cid in chain_ids:
if cid in seen_ids:
new_id = next_chain_id(cid)
while new_id in seen_ids or new_id in chain_ids:
new_id = next_chain_id(new_id)
session.logger.info(
f"Remapping chain ID {cid} in #{s.id_string} to {new_id}")
chain_id_mapping[cid] = new_id
seen_ids.add(new_id)
else:
seen_ids.add(cid)
target.combine(s, chain_id_mapping, target.scene_position)
def launch_rotamers(self):
from chimerax.atomic import selected_residues
sel_residues = selected_residues(self.session)
if not sel_residues:
raise UserError("No residues selected")
num_sel = len(sel_residues)
if num_sel > 10:
from chimerax.ui.ask import ask
confirm = ask(
self.session,
"You have %d residues selected, which could bring up %d"
" rotamer dialogs\nContinue?" % (num_sel, num_sel),
title="Many Rotamer Dialogs")
if confirm == "no":
return
res_type = self.res_type_option.value
from chimerax.core.commands import run, StringArg
from chimerax.rotamers import NoResidueRotamersError
lib_name = StringArg.unparse(self.rot_lib_option.value)
try:
run(self.session,
"swapaa interactive sel %s rotLib %s" % (res_type, lib_name))
except NoResidueRotamersError:
run(self.session, "swapaa sel %s rotLib %s" % (res_type, lib_name))
def criteria(self, session):
from chimerax.atomic import selected_residues
return len([
r for r in selected_residues(session)
if r.polymer_type == r.PT_AMINO
]) == 1
