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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
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