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° | BuildRes | - | Build single residue |
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| | | Command | | Argument | | Datatype | | Default | | Min | | Max | |
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| Format 1: | | BuildRes | Name = Amino acid residue name, | | STRING | | - | | - | | - | | |
| | Psi = Psi angle in degrees, |
| FLOAT | | 180.0 | | - | | - | | |||
| | Center = Yes | No | | STRING | | Yes | | - | | - |
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| Format 2: | | BuildRes | Name = Nucleotide residue name, | | STRING | | - | | - | | - | | |
| | Alpha = Alpha angle in degrees, | | FLOAT | | -46.85 | | - | | - | | |||
| | Beta = Beta angle in degrees, | | FLOAT | | -146.06 | | - | | - | | |||
| | Gamma = Gamma angle in degrees, |
| FLOAT | | 36.41 | | - | | - | | |||
| | Center = Yes | No | | STRING | | Yes | | - | | - |
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| Python: | | result = BuildRes(name,psi=None,center=None) result = BuildRes2(name,alpha=None,beta=None,gamma=None,center=None) |
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| Menu: | | Edit > Build > Residue | | ||||||||||
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| Related: | | BuildMol , BuildAtom, AddRes | | ||||||||||
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| Required: | |  | |
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The BuildRes
command creates a single amino acid or nucleotide residue with the specified name as a new object.
After building the first residue with BuildRes
, you can use AddRes to extend the peptide or nucleic acid.
Depending on the chosen residue name, the command expects a different selection of dihedral angles.
Building an amino acid:
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.
# EXAMPLE: BUILD A HELIX OF ALANINES phi = -50 psi = -50 # BUILD THE FIRST RESIDUE peptide = BuildRes Ala,(psi) # EXTEND THE PEPTIDE for i=2 to 10 AddRes Ala,(peptide),Phi=(phi),Psi=(psi)
Building a nucleotide:
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 Alpha, Beta and Gamma
are described in more detail here.
Example 1:
BuildRes Name=Arg,Psi=50
Build a new object consisting of one arginine residue with a carboxyl terminus and a Psi angle of
50 degrees.
Example 2:
BuildRes Name=DA,Alpha=-40,Beta=135,Gamma=35
Build a new object consisting of one deoxy-adenosine nucleotide in standard B-DNA conformation.
Example 3:
obj = BuildRes Cys
Build a new object consisting of one cysteine residue with a carboxyl terminus and a Psi angle of
180 degrees and assign its number to variable 'obj'.
Example macro:
# EXAMPLE BuildRes # Requires YASARA Model Clear BuildRes His,Psi=50 BallStickAtom Sidechain Pos Z=5
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| Figure: Result of the example macro above. |