[Open Babel] Re: mol conversion not defaulting to v2000

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[Open Babel] Re: mol conversion not defaulting to v2000

Geoffrey Hutchison
Hi James,

This is not a bug.

MDL Molfile v2000 cannot store more than 999 atoms. If you're trying  
to convert a protein with 5828 atoms, you simply *have* to use v3000  
in order to store everything. Open Babel is doing the correct thing  
here.

Arguably, it should explain this to you when you try to force the  
v2000 format, but it is the correct behavior.

Cheers,
-Geoff

On Oct 28, 2005, at 9:45 AM, Dr J Smith wrote:

>
> Hi Geoff
>
> I'm using 2.0.0b5-20051001
>
> I notice that
> babel  -ipdb abc.pdb -omol abc.mol
>
> doesn't default to v2000 as specified by -Hmol
> and the -x2 swicg doens't work when I do
>
> babel  -x2 -ipdb abc.pdb -omol abc.mol
> I have a protein with 5828 atoms.
>
> Thought you should know,
> Regards
> James
>
> --
> ________________________________
> Dr James Smith
> Computer-Chemie-Centrum
> Univeristaet Erlangen-Nuernberg
> Naegelsbachstrasse 25
> 91052 Erlangen
> Germany
>
> http://www.chemie.uni-erlangen.de/clark/smith/
> ________________________________
>



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