Modelling
flat.modelling
Module for modelling molecular objects.
- flat.modelling.add_missing_atoms(selection, sculpt=False, cycles=100, *, _self=cmd)
- DESCRIPTION
Mutate those residues to themselves which have missing atoms.
- USAGE
add_missing_atoms selection [, sculpt [, cycles ]]
- ARGUMENTS
- selectionstring
Atom selection.
- sculptbool, default = False
Sculpt inserted residue.
- cyclesint, default = 100
Number of sculpting cycles.
- SOURCE
From PSICO (c) 2010-2012 Thomas Holder, MPI for Developmental Biology
- flat.modelling.fix_h(selection='all', *, _self=cmd)
- DESCRIPTION
Adds hydrogens with correct names onto a molecule using OpenMM based on known templates.
Note
It’s a kludge and may need some love and persuasion to work. This adds hydrogens based on template i.e. it will most likely only work for proteins, sugars, and DNA/RNA. Also needs to have well defined C- and N-terminus.
- USAGE
fix_h [ selection ]
- ARGUMENTS
- selectionstr, optional
Atom selection.
- flat.modelling.mutate(selection, name, sculpt=0, cycles=100, *, _self=cmd)
- DESCRIPTION
Mutate a single residue and select best rotamer. Optionally fit lowest energy mutant rotamer to structure.
- USAGE
mutate selection, name [, sculpt [, cycles ]]
- ARGUMENTS
- selectionstring
atom selection to renumber.
- namestr
Name of fragment to insert.
- sculptbool, default = False
Sculpt inserted residue.
- cyclesint, default = 100
Number of sculpting cycles.
- SEE ALSO
- flat.modelling.relax(selection, backbone=True, neighbors=True, cycles=1000, state=0, *, _self=cmd)
- DESCRIPTION
Relax the given selection using sculpting wizard.
- USAGE
relax selection [, backbone [, neighbors [, cycles [, state ]]]]
- ARGUMENTS
- selectionstr
Atom selection.
- backbonebool, default = True
Include backbone in sculpting (opposed to side-chains only).
- neighborsbool, default = True
Include atoms near (6 Angstroms) to selection in sculpting.
- cyclesint, default = 1000
Number of sculpting cycles.
- stateint, default = 0
Object state.
- flat.modelling.replace(selection, name, sculpt=True, cycles=100, *, quiet=1, _self=cmd)
- DESCRIPTION
Replace target residue with fragment. Use for ONLY for non-standard residues.
- USAGE
insert selection, name [, sculpt [, cycles ]]
- ARGUMENTS
- selectionstr
Atom selection.
- namestr
Name of fragment.
- sculptbool, default = True
Sculpt inserted residue.
- cyclesint, default = 100
Number of sculpting cycles.
- SEE ALSO
- flat.modelling.sbond(atom1='(pk1)', atom2='(pk2)', length=2.0, state=1, cycles=1000, *, _self=cmd)
- DESCRIPTION
Bond two selected atoms and relax the structure. Use the PkAt mouse action (typically, Ctrl + middle-click).
- USAGE
sbond [ atom1 [, atom2 [, length [, state, [, cycles ]]]]]
- ARGUMENTS
- atom1, atom2str, default = ‘(pk1)’, ‘(pk2)’
Atom selection to bond.
- lengthfloat, default = 2.0
Bond length in Angstroms.
- stateint, default = 1
Selected state.
- cyclesint, default = 1000
Number of sculpt iterations.
- flat.modelling.sculpt_homolog(mobile, target, state=1, cycles=1000, fix='restrain', *, quiet=1, _self=cmd)
- DESCRIPTION
Sculpt mobile towards target, based on sequence alignment.
- USAGE
sculpt_homolog mobile, target [, state [, cycles [, fix ]]]
- ARGUMENTS
- mobile, targetstr
Atom selection of mobile and target.
- stateint, default = 1
Select state
- cyclesint, default = 1000
Number of sculpt iterations.
- fixstr, default = ‘restrain’
Method for fixing updated atoms: restrain, fix, protect, none.
- SOURCE
From PSICO(c) 2010-2012 Thomas Holder, MPI for Developmental Biology
- flat.modelling.update_align(mobile, target, state=1, fix='none', *, quiet=1, _self=cmd)
- DESCRIPTION
Update (and optionally fix) coordinates based on sequence alignment.
- USAGE
update_align mobile, target [, state [, fix ]]
- ARGUMENTS
- mobile, targetstr
Atom selection of mobile and target.
- stateint, default = 1
Select state
- fixstr, default = ‘none’
Method for fixing updated atoms: restrain, fix, protect, none.
- SOURCE
From PSICO (c) 2010-2012 Thomas Holder, MPI for Developmental Biology