[Chimera-users] Generating a PDB file

Aldo Segura aldosegura at gmail.com
Thu Sep 19 11:34:20 PDT 2013

Dear Nathalia,

1) How do you save your pdb file (ligand and receptor included). Did you
select the "single file" option at the bottom the save menu?
2) How looks your pdb file in a text editor (worpad for windows or gedit in
Linux)? I'm not sure, somebody correct me if I'm wrong, when you are trying
to merge two pdb files Chimera introduces some legends ("model") into the
pdb file to indicate who is the pdb 1 and pdb 2, respectively. You should
try (using your text editor) to find those legends and removing them from
the pdb file, save the changes, then, you should be able to open your file
in Pymol.

Best regards,


Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
e-mail: Aldo.Segura-Cabrera at cchmc.org <asegurac at ipn.mx>;
aldosegura at gmail.com
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