Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows

[Greg L. <gre...@gm...>]

On Mon, Nov 25, 2013 at 5:10 AM, Greg Landrum <gre...@gm...>wrote:

>
>
>>  Another problem is that I cannot read pdbs containing metals (e.g. 1vj5)
>>
>>
>>
>> Is there any workaround for that problem? I hope you can help me…
>>
>
> That bug is reproducible on linux as well. The normal solution to this
> would be to skip the sanitization step that causes the error, but
> unfortunately it seems that also causes the PDB parser to fail. I'll take a
> look at fixing it.
>

I've now fixed the problem with not being able to skip sanitization, but I
am still stuck on this particular protein.
1VJ5 has a Mg atom (#4333) with CONECT records to six other atoms. This
leads to a valence on Mg that is higher than the RDKit normally accepts.

How should this type of situation be handled by the PDB parser?

The irony of a PDB file wth *too many* CONECT records is killing me. :-)

-greg