[Chimera-users] PDB opens distorted

Francesco Pietra chiendarret at gmail.com
Fri Aug 27 08:35:58 PDT 2010

I have drawn a slightly modified small peptide (terminal phenylalanine
changed to phenylalanine-amide)  with an old, efficient package
(PCMODEL). I have drawn from from either amino acid templates or
atom-per-atom and then saved as pdb. In case of drawing atom-per-atom,
I have edited the residue names, changing UNK to the appropriate
standard amino acid name, except phenylalanine-amide, named PHA).

Opening the pdb file with an editor, the atoms are often scattered,
not sequentially grouped together for a given amino acid.

Well, both the non-edited and the edited pdb files open correctly with
either PCMODEL of VMD, not with CHIMERA. In the latter case, incorrect
bonds between the atoms are seen, and the molecule is compressed.
Deleting all CONECT  generated by PCMODEL was even worse for CHIMERA.

With non peptidic molecules I never went into such troubles using the
same packages.

Thanks for suggestions how to rearrange the pdb for CHIMERA.

francesco pietra

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