def run_script(session):
from chimerax.atomic import selected_atoms
from chimerax.build_structure import modify_atom
from chimerax.build_structure.mod import ParamError
from chimerax.core.errors import UserError
sel = selected_atoms(session)
if len(sel) != 1:
raise UserError('Please select a single atom!')
sel = sel[0]
current_num_bonds = len(sel.neighbors)
current_color = sel.color
try:
modify_atom(sel,
sel.element,
current_num_bonds + 1,
connect_back=False,
res_name=sel.residue.name)
sel.color = current_color
except ParamError as e:
# If modify_atom throws an error at the previous step, it will have deleted
# any attached hydrogens and not put them back. We need to put them back here.
modify_atom(sel,
sel.element,
current_num_bonds,
connect_back=False,
res_name=sel.residue.name)
sel.color = current_color
raise UserError(str(e))
def add_oxt(session, residue):
catom = residue.find_atom('C')
resname = residue.name
if catom is None:
session.logger.warning('Residue {} {}{} has no C atom!'.format(
residue.name, residue.chain_id, residue.number))
return
color = catom.color
for n in catom.neighbors:
if n.name == 'OXT':
session.logger.warning(
'Chain {} already has a C-terminal OXT. Skipping.')
return
if n.residue != residue:
raise UserError(
'Residue {} {}{} is not a C-terminal residue!'.format(
residue.name, residue.chain_id, residue.number))
from chimerax.build_structure import modify_atom
from chimerax.atomic import Element
atoms = modify_atom(catom, catom.element, 3, res_name=residue.name)
for a in atoms:
if a.element.name == 'H':
break
modify_atom(a,
Element.get_element('O'),
1,
name='OXT',
res_name=residue.name)
catom.color = color
session.logger.info('Added a C-terminal OXT to chain {}'.format(
residue.chain_id))
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 break_disulfide(cys1, cys2):
from chimerax.core.errors import UserError
from chimerax.atomic import Atoms
s1 = cys1.find_atom('SG')
s2 = cys2.find_atom('SG')
if s1 is None or s2 is None:
raise UserError(
'Missing SG atom! Are both residues complete cysteines?')
if s2 not in s1.neighbors:
raise UserError('These residues are not disulfide bonded!')
has_hydrogens = ('H' in cys1.atoms.element_names)
b = Atoms((s1, s2)).intra_bonds[0]
b.delete()
if has_hydrogens:
from chimerax.build_structure import modify_atom
modify_atom(s1, s1.element, 2, res_name='CYS', connect_back=False)
modify_atom(s2, s2.element, 2, res_name='CYS', connect_back=False)
def add_missing_md_template_atoms(session, residue, md_template,
residue_indices, template_indices):
import numpy
template_extra_indices = [
i for i in range(len(md_template.atoms)) if i not in template_indices
]
if not len(template_extra_indices):
return
template_extra_bonds = set([
b for b in md_template.bonds
if any([i in template_extra_indices for i in b])
])
from collections import defaultdict
stub_map = defaultdict(list)
# stub_map maps an existing atom in the residue to any atoms in the MD
# template that should be connected to it, but aren't yet modelled.
found_bonds = set()
for b in template_extra_bonds:
i1, i2 = b
i1_index = numpy.where(template_indices == i1)[0]
i2_index = numpy.where(template_indices == i2)[0]
if not len(i1_index) and not len(i2_index):
continue
if len(i2_index):
i1, i2 = i2, i1
i1_index = i2_index
i1_index = i1_index[0]
res_atom = residue.atoms[residue_indices[i1_index]]
# if not res_atom:
# raise RuntimeError("Atom {} should be in residue, but isn't".format(ccd_atom.name))
stub_map[res_atom].append(i2)
found_bonds.add(b)
template_extra_bonds = template_extra_bonds.difference(found_bonds)
if len(template_extra_bonds):
err_str = (
'MD template {} for residue {} {}{}{} contains extra atoms that are not in '
'a coordinate template, and are not directly connected to existing '
'atoms. Since MD templates do not explicitly provide geometry,'
'these atoms will not be built.').format(md_template.name,
residue.name,
residue.chain_id,
residue.number,
residue.insertion_code)
session.logger.warning(err_str)
seen = set()
for new_atom_list in stub_map.values():
for i in new_atom_list:
if i in seen:
err_str = (
'The atom {} in MD template {} bonds to more than '
'one existing atom in residue {}. Since MD templates do '
'not explicitly specify geometry, this type of atom addition '
'is not currently supported. The resulting residue will '
'contain only those atoms which the MD and coordinate templates '
'have in common').format(md_template.atoms[i].name,
md_template.name, residue.name)
raise UserError(err_str)
seen.add(i)
from chimerax.atomic import Element
from chimerax.build_structure import modify_atom
for existing_atom, new_indices in stub_map.items():
num_new_atoms = len(new_indices)
num_existing_neighbors = len(existing_atom.neighbors)
num_bonds = len(existing_atom.neighbors) + num_new_atoms
new_tatoms = [md_template.atoms[i] for i in new_indices]
from chimerax.build_structure.mod import ParamError
try:
modified_atoms = modify_atom(existing_atom,
existing_atom.element,
num_bonds,
res_name=residue.name)
except ParamError:
err_str = (
'Failed to add atoms {} to atom {} because this will '
'lead to having {} atoms attached, which is more than its '
'assigned geometry can support. This is probably due to an '
'error in the MD template ({}). If this template is built '
'into ISOLDE, please report this using Help/Report a bug'
).format([a.name for a in new_tatoms], existing_atom.name,
num_existing_neighbors + len(new_tatoms),
md_template.name)
raise UserError(err_str)
new_atoms = modified_atoms[1:]
for na, ta in zip(new_atoms, new_tatoms):
modify_atom(na,
Element.get_element(ta.element.atomic_number),
1,
name=ta.name,
res_name=residue.name)