-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPvizQUxlJ7aRr7hoRAo72AJ9D8agKfA1SNe6goUAI+etm9CIC7wCg+KEJ ZyCDiGCgBkEnA7nngqjeVeU= =GG6n -----END PGP SIGNATURE-----
