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° | AddRes | - | Add terminal residue |
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| | | Command | | Argument | | Datatype | | Default | | Min | | Max | |
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| Format 1: | | AddRes | Name = Amino acid residue name, |
| STRING | | - | | - |
| - | | |
| | Object selection, | | SELECTION | | - | | - | | - | | |||
| | Omega = Omega angle in degrees, | | FLOAT | | 180.0 | | - | | - | | |||
| | Phi = Phi angle in degrees, | | FLOAT | | 180.0 | | - | | - | | |||
| | Psi = Psi angle in degrees |
| FLOAT | | 180.0 | | - | | - | | |||
| Format 2: | | AddRes | Name = Nucleotide residue name, | | STRING | | - | | - | | - | | |
| | Object selection, | | SELECTION | | - | | - | | - | | |||
| | Epsilon = Epsilon angle to previous residue in degrees, | | FLOAT | | 155.0 | | - | | - | | |||
| | Zeta = Zeta angle to previous residue in degrees , | | FLOAT | | -95.18 | | - | | - | | |||
| | Alpha = Alpha angle in degrees, | | FLOAT | | -46.85 | | - | | - | | |||
| | Beta = Beta angle in degrees, | | FLOAT | | -146.06 | | - | | - | | |||
| | Gamma = Gamma angle in degrees |
| FLOAT | | 36.41 | | - | | - | | |||
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| Python: | | AddRes(name,selection1,omega=None,phi=None,psi=None) AddRes2(name,selection1,epsilon=None,zeta=None,alpha=None,beta=None,gamma=None) |
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| Menu: | | Edit > Add > to soup: Residue |
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| Related: | | BuildRes, BuildMol | | ||||||||||
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| Required: | |  | |
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The AddRes
command adds an amino acid to the C-terminal end, or a nucleotide to the 3' end of the selected object,
using the specified dihedral angles.
Depending on the chosen residue name,
the command expects a different selection of dihedral angles.
Building peptides:
The residue
name can be any of the 20 amino acids in three letter code, as well as one of the special residue names
listed here.
The
Phi / Psi angles corresponding to the various secondary structure types can be found here.
Omega
is the dihedral angle of the peptide bond, usually 180 degrees for trans- and 0 degrees or cis-peptide bonds.
After building the first residue with BuildRes
, you can use AddRes to extend the peptide,
forming any secondary structure you want:
# EXAMPLE: BUILD A HELIX WITH A GIVEN SEQUENCE phi = -50 psi = -50 sequence = 'Ser','Ile','Val','Ala','Arg','Ser','Asn','Phe','Asn','Val','Cys' # BUILD THE FIRST RESIDUE peptide = BuildRes (sequence(1)),(psi) # EXTEND THE PEPTIDE for i=2 to count sequence AddRes (sequence(i)),(peptide),Phi=(phi),Psi=(psi)
Building nucleic acids:
The residue name can be any of the four RNA nucleotides A, U, G and C,
or one of the four DNA deoxy-nucleotides DA, DT, DG and DC. The latter four residue names match the new PDB format version
3.0.
The dihedral angles Epsilon and Zeta define the conformation of the newly added residue with respect to the previous residue and are therefore specified first
(in the figure below, they would be just above Alpha, not where they are indicated),
while Alpha, Beta and Gamma are internal dihedral angles as shown in the figure below:
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| Figure: Backbone dihedral angles in nucleotides. Saenger W., Principles of Nucleic Acid Structure, Springer New York 1984 |
Different DNA/RNA conformations can be built using these sets of default dihedral angles
(the Delta and Chi dihedrals are not modified by this command):
| Structure type | Alpha | Beta | Gamma | Delta | Epsilon | Zeta | Chi |
| B-DNA (YASARA) | -46.85 | -146.06 | 36.41 | 156.38 | 155 | -95.18 | -97.8 |
| RNA (YASARA) | -66.8 | 153 | 68.1 | 82.4 | -140 | -75.4 | -173 |
| A-DNA (fibres) | -50 | 172 | 41 | 79 | -146 | -78 | -154 |
| GGCCGGCC | -75 | 185 | 56 | 91 | -166 | -75 | -149 |
| B-DNA (fibres) | -41 | 136 | 38 | 139 | -133 | -157 | -102 |
| CGCGAATTCGCG | -63 | 171 | 54 | 123 | -169 | -108 | -117 |
| Z-DNA (C residues) | -137 | -139 | 56 | 138 | -95 | 80 | -159 |
| Z-DNA (G residues) | 47 | 179 | -169 | 99 | -104 | -69 | 68 |
| DNA-RNA decamer | -69 | 175 | 55 | 82 | -151 | -75 | -162 |
| A-RNA | -68 | 178 | 54 | 82 | -153 | -71 | -158 |
(Blackburn and Gait, Nucleic acids in chemistry and biology,
Oxford University Press New York 1996. Many thanks to IMB Jena for compiling this information.
Note: except for the first two entries, the table above is reproduced without validation).
Example 1:
AddRes Lys,1crn,Phi=50,Psi=50
Add a lysine residue to the C-terminus of object 1crn, with angles Omega/Phi/Psi
= 180/50/50.
Example 2:
AddRes DA,Strand1,Epsilon=155,Zeta=-95,Alpha=-47,Beta=-146,Gamma=36
Add a deoxy-adenosine residue to the 3' end of object strand1,
using a classic B-DNA conformation.