makestructure
Modify structure by applying dihedral values to specified residues.
makestructure <List of Args>
Apply dihedrals to specified residues using arguments found in <List of Args>, where an argument is 1 or more of the following arg types:
<sstype keyword>:<res range>
Apply secondary structure type (via phi/psi backbone angles) to residues in given range. If the secondary structure type is a turn, the residue range must correspond to a multiple of 2 residues.
| Keyword | phi, psi (deg.) | # residues |
| alpha | -57.8, -47.0 | 1 |
| left | -57.8, 47.0 | 1 |
| pp2 | -75.0, 145.0 | 1 |
| hairpin | -100.0, 130.0 | 1 |
| extended | -150.0, 155.0 | 1 |
| typeI | -60.0, -30.0 | -90.0, 0.0 | 2 |
| typeII | -60.0, 120.0 | 80.0, 0.0 | 2 |
| typeVIII | -60.0, -30.0 | -120.0, 120.0 | 2 |
| typeI’ | 60.0, 30.0 | 90.0, 0.0 | 2 |
| typeII | 60.0, -120.0 | -80.0, 0.0 | 2 |
| typeVIa1 | -60.0, 120.0 | -90.0, 0.0 | 2 |
| typeVIa2 | -120.0, 120.0 | -60.0, 0.0 | 2 |
| typeVIb | -135.0, 135.0 | -75.0, 160.0 | 2 |
<custom ss>:<res range>[:<phi>:<psi>]
If <phi> and <psi> are given, define a custom secondary structure conformation named <custom_ss> and apply to residues in range. If <custom_ss> has been previously defined then apply it to residues in range.
<custom turn>:<res range>[:<phi1>:<psi1>:<phi2>:<psi2>]
If <phi1>, <psi1>, <phi2>, and <psi2> are given, defined a custom turn conformation named <custom_turn> and apply to residues in range (range must correspond to a multiple of 2 residues). If <custom_turn> has been previously defined then apply it to residues in range.
<custom dih>:<res range>[:<dih type>:<angle>]
<dih type> = phi psi chip omega alpha beta gamma delta epsilon zeta nu1 nu2 chin
If <dih type> and <angle> are given, apply <angle> to selected dihedrals of type in range. If <custom dih> has been previously defined then apply it to residues in range.
<custom dih>:<res range>[:<at0>:<at1>:<at2>:<at3>:<angle>[:<offset>]]
Apply <angle> to dihedral defined by atoms <at1>, <at2>, <at3>, and <at4>, or use previously defined <custom_dih>.
| <offset> | Description |
| -2 | <at0> and <at1> in previous residue. |
| -1 | <at0> in previous residue. |
| 0 | All atoms in single residue. |
| 1 | <at3> in next residue. |
| 2 | <at2> and <at3> in next residue. |
ref:<range>:<refname>[:<ref range>]
Apply dihedrals from residues <ref_range> in previously loaded reference structure <refname> to dihedrals in <range>.
Examples
Assign polyproline II structure to residues 1 through 13:
makestructure pp2:1-13
Make residues 1 and 12 ’extended’, residues 6 and 7 a type I’ turn, and two custom assignments, one (custom1) for residues 2-5, the other (custom2) for residues 8-11:
makestructure extended:1,12 \ custom1:2-5:-80.0:130.0:-130.0:140.0 \ typeI’:6-7 \ custom2:8-11:-140.0:170.0:-100.0:140.0
Assign residue 5 phi 90 degrees, residues 6 and 7 phi=-70 and psi=60 degrees:
makestructure customdih:5:phi:90 custom:6,7:-70:60
Create a new dihedral named chi1 and assign it a value of 35 degrees in residue 8:
makestructure chi1:8:N:CA:CB:CG:35
Assign ’extended’ structure to residues 1 and 12, a custom turn to residues 2-5 and 8-11, and a typeI’ turn to residues 6-7:
makestructure extended:1,12 \ custom1:2-5:-80.0:130.0:-130.0:140.0 \ typeI’:6-7 \ custom1:8-11
Assign secondary structure from reference structure:
parm ../tz2.parm7 reference ../tz2.rst7 trajin pp2.rst7.save makestructure "ref:1-13:tz2.rst7" rmsd reference trajout fromref.pdb multi