Indeed I wrote those scripts to do just that.
They are meant to start with an existing PDB file and then tack on new
atoms or tweak existing ones. You just concatenate the PDB file itself
either before or after the "BUILD" command lines and it sends the edited
structure to stdout. The only exception is build_n2c.awk, which needs
the atoms to come before the build commands. This is because the
build_n2c.awk program can and will start with nothing. In that case it
puts the first CA at 0,0,0 and goes from there. Only problem is you can
only put 2841 residues in a row as an extended chain before your z
coordinate gets bigger than 9999 A, and that exceeds the representation
in the pdb. If you really want an extended chain I recommend starting
with a template near the negative corner of this 10998 A edge cube that
every PDB lives inside.
-James Holton
MAD Scientist
On 4/5/2025 7:48 AM, Edward Berry wrote:
I think James Holton's "build_pdb" project can do this.
For example, to make a canonical alpha helix,
#!/bin/csh
cat << EOF | build_n2c.awk | tee helix.pdb
BUILD MET 0 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD ALA -57 -47 180
BUILD -57
EOF
I understand it can also add side chains, with default rotamers or
specified chi angles.
and start at either end of a pre-existing pdb file.
https://github.com/jmholton/build_pdb
Carter, Charlie wrote on 4/4/2025 6:27 AM:
Does anyone know if there is a program that will take a sequence file
associated with phi and psi angles and produce a 3D coordinate set in
pdb format?
I know this can be done in the sense that Byron Rubin’s bender did
the same thing in analog fashion.
Many thanks
Charlie Carter
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