Biomolecular Assembly view

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Gibbo
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Joined: 09/09/2011
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I've been struggling with a pdb file that only shows the asymmetric unit in Molecules rather than the biomolecular assembly. I can download the gz file from the pdb onto the desktop Mac and transfer to molecules. However, opening the file shows the asymmetric unit. I think that downloading the file directly into molecules has a similar outcome.

I've also had similar issues with desktop packages (imol, jmol, Accelerys viewer). I'd like to use the file in lectures on the ipad, so any help would be welcomed.

Cheers,
Gibbo

Brad Larson
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Joined: 05/14/2008
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Is the assembly composed of multiple structures? Currently, I only display the first structure contained within the PDB file. Many PDB files have multiple NMR structures, etc. and I just haven't worked something into the interface to select the appropriate one.

If you could somehow alter the PDB so that each of the components in the assembly was considered part of the same structure, it should display them all (assuming the whole thing fits in memory on the device).

Gibbo
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Joined: 09/09/2011
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Many thanks Brad for the suggestion.

The solution was to open the .gz file in Chimera so as to view both strands of the A-DNA. Saved it as a Mol2 file. This I opened in iMol and saved it as a PDB file which was readable by molecules on the iPad.

The problem was that the PDB files downloaded from the PDB was just the asymmetric unit, a single strand of the duplex A-DNA. The file with the biomolecular assembly (both strands of the duplex DNA) was a .gz file which most of my desktop viewing applications just showed one strand.

It was only Chimera that could correctly display the .gz file.

Thanks again for the help.

Gibbo

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