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

[Julia W. <we...@ph...>]

Hi Greg,

I'm using the 64bit version of the RDKit on Windows 7 Professional (64bit).

Kind regards

Julia

Von: Greg Landrum [mailto:gre...@gm...]
Gesendet: Montag, 25. November 2013 05:11
An: Julia Weber
Cc: Rdk...@li...
Betreff: Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows

Hi Julia,

On Fri, Nov 22, 2013 at 11:14 AM, Julia Weber <we...@ph...<mailto:we...@ph...>> wrote:

it seems that it is not possible to read a PDB file after you have read a sdf file. I don't see this problem on Linux.

To help narrow the problem down: are you using the 32bit or 64bit version of the RDKit on windows?

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.

-greg