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 <baoille...@gmail.com> 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 <j...@drugdiscoveryathome.com>: >> 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 >> >> [boinc...@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 >> [boinc...@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 >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >> trial. Simplify your report design, integration and deployment - and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org
test.pdb
Description: Protein Databank data
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