I have a molecule in cif format and am trying to generate the unit cell using command
babel -i cif mol.cif -o pdb out.pdb --unitcell fillUC. I am getting proper output, but the atom label is gone missing. In fact the atom label in the pdb file format is replaced by atom type. For example, CA is replaced by C only. Any suggestion for getting the proper atom label?
Your given command works reasonably on three CIFs I tried it on, (albeit with curious variants between 'babel' and 'obabel' as to where the output ended up). Insofar as every residue assigned its proper 'C' and 'CA' atom. Is there any chance that your input CIF is the source of the problem? (being mislabeled itself, or even lacking any amino acid residues somehow?)
You use Mercury 3.3 from http://www.ccdc.cam.ac.uk/mercury/. Open your .CIF file using Mercury 3.3 and check for atom labels.
Then save the .CIF file as .pdb file. Then open the .pdb file using Mercury 3.3 and check for atom labels. I hope this method will work nicely.
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