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Dear Eike,
did you try surface/volume without any extra options? That should work
with a few lines of code, e.g.
surface xyzin1 yourfile.pdb xyzout yourfile.surface << eof1
RUN
STOP
eof1
volume xyzin yourfile.surface << eof2 | tee volume.log
RUN
eof2
Probably prints the total volume somewhere in volume.log
You could also try matthews_coeff which gives you the percentage of
the unit cell volume based on the sequence, although I am not aware
whether it can take RNA/protein mixes into account. Its precision is
probably close enough to a realistic estimate.
Cheers,
Tim
On 05/24/12 14:11, Eike Schulz wrote:
> Hello everyone,
>
> I am working on protein RNA complex and would like to verify the
> oligomeric state from the crystal structure by analytical
> ultracentrifugation (AUC). To fit data from AUC we need a good
> estimate of the partial specific volume of the complex, therefore I
> wanted to retrieve this value from my pdb coordinates, in either of
> the oligomeric states.
>
> My idea was to calculate the volume of the complex: - I had a look
> at rwcontents but this gave me only the volume of the cell and not
> of the protein itself - AreaImol does not report the volume (?) - I
> also had a look at SURFACE/VOLUME but found it quiet cryptic.
>
> Are there other ways to calculate the volume of a protein/complex
> from pdb-coordinates, maybe an alternative to SURFACE/VOLUME? Or is
> there some software that directly reports the partial specific
> volume?
>
> Many thanks in advance
>
> Eike
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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