Reply – Re: Filter PDB with COMPND Identifier
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Re: Filter PDB with COMPND Identifier
— by Jack Shultz-2 Jack Shultz-2
Noel,

The main file is too big to send. Here is a file with 2 structures. I
don't see any examples for using --seperate
I tried doing this without and success
babel test.pdb out.pdb --separate

On Sat, Nov 21, 2009 at 2:59 PM, Noel O'Boyle <[hidden email]> wrote:

> 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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>


--
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org

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