Reply – Re: Filter PDB with COMPND Identifier
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Re: Filter PDB with COMPND Identifier
— by Noel O'Boyle Noel O'Boyle
Your usage of babel --filter is correct, however it won't work on a
PDB file as the entire PDB file is regarded by OpenBabel as a single
"Molecule". It's a good idea though, and maybe something we should
think about implementing. Feel free to file a feature request at
http://sourceforge.net/tracker/?atid=428743&group_id=40728&func=browse

You didn't attach the PDB file so I can't test this, but you might
want to try the --separate option to split the PDB into disconnected
fragments.

- Noel

2009/11/20 Jack Shultz <[hidden email]>:

> Trying to filter a PDB file starting with this compound
>
> COMPND    omega_1
> HETATM    1  C1  UNL     1       1.852  -3.133   1.682  1.00  0.00           C
> HETATM    2  C2  UNL     1       0.996  -2.034   1.424  1.00  0.00           C
> HETATM    3  C3  UNL     1       2.869  -2.681   2.494  1.00  0.00           C
>
> I tried it two ways
>
> [boincadm@vps Ambinter_LL_3D_1-1]$ babel -ipdb Ambinter_LL.pdb -opdb
> omega_1.pdb --filter "COMPND='omega_1'"
> 0 molecules converted
> 52 info messages 12 audit log messages
> [boincadm@vps Ambinter_LL_3D_1-1]$ babel -ipdb Ambinter_LL.pdb -opdb
> omega_1.pdb --filter "title='omega_1'"
> 0 molecules converted
> 52 info messages 12 audit log messages
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>
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