builder.md

This section describes how to build peptides and dna strands. There are several possibilities to do this.

Proteins

Constructing amino acids

Let's start by building a single aminoacid.

>>> from pmx import *
>>> mol = Molecule().new_aa( "ALA")          # build alanine

if we wish to build a peptid chain starting with this residue we first have to initialize the peptide chain

>>> c = Chain( residues = [mol] )               # build peptide chain

now we can extend this chain either at the n-terminus or at the c-terminus

>>> c.nbuild("T")                    # extend at n-terminus
>>> c.cbuild("R")                   # extend at c-terminus

if this is all we want to, we simply write the chain as pdb file

>>> c.write("TAR.pdb")

Building peptide chains from sequence

usually we have a peptide sequence to be transformed to 3d coords. This can be done from the chain level

>>> sequence = "FRTLKNCWQ"
>>> c = Chain().create( sequence )
>>> c.write("extended_pep.pdb")

This builds a peptide chain in an extended conformation.

Changing secondary structure

If we now want to change the peptide conformation we can change the backbone dihedral angles for each residue. E.g., the phi/psi angles for an ideal alpha-helix are -57 and -47 degree.

>>> for resi in c.residues:
>>>      resi.set_phi( -57, True )
>>>      resi.set_psi( -47, True )
>>> c.write("helix_pep.pdb")

transforms the peptide into a helical conformation.

Chain fusion

We can also attach a new series of peptides to the helix peptides, either by using the nbuild() or cbuild() functions or by creating a new chain from scratch that should be fused with the first one

So let's first build a new chain

>>> c2 = Chain().create("LMNFRTS")

and attach this peptide to the helix peptide

>>> c.fuse( c2 )
>>> c.write( "fused_pep.pdb")

Chain c2 is now merged into chain c. Creating chains of repeating units

Changing secondary structure If we would like to construct a chain of repeating units, this can also be done in a straightforward manner. We simply construct the repeating unit and extend by copies of itself.

>>> rep_seq = "HEATLLFT"
>>> c = Chain().create(rep_seq)

now we create a copy of this chain

>>> new_chain = c.copy()

and attach the new chain 5 times

>>> for i in range(5): 
>>>     c.fuse( new_chain.copy() )
>>> c.write("repeat_pep.pdb")
>>> print c.sequence()
HEATLLFTHEATLLFTHEATLLFTHEATLLFTHEATLLFTHEATLLFT

and finally set some residues in helical conformation

>>> helical_residues = c.fetch_residues(["HIS","GLU","ALA","THR","LEU"])
>>> for resi in helical_residues:
>>>    resi.set_phi( -57, True )
>>>    resi.set_psi( -47, True )
>>> c.write("repeat_helix.pdb")

DNA

There is not much functionality regarding DNA up to now. Just a simple DNA builder.

Building DNA strands

This requires the pmx.builder module

>>> from pmx.builder import *
>>> model = build_dna_strand("ACGTGTCA")
>>> model.write("dna.pdb")