Hi Manish, But then volume is biased by the plot grid size one chooses and not the converged volume. In short, one isn't even using the results of volume refinement because one'd get the same answer from the same grid size for the same orientation (given the same probe radius). Using the final converged volume (ie, the last value in the table above Nr of cycles/average/sigma line in output file), as Dr. Mayer says, should be more correct.
If it is only a % change of cavity volume on binding of ligand one is looking for, it MAY not make a difference. I am not too sure about that though. I haven't averaged the volumes both ways and compared the ratios. Thanks to everyone who replied and everyone who read the exchanges! Sangeetha. On Wed, Aug 20, 2008 at 10:24 AM, <[EMAIL PROTECTED]> wrote: > Hi, > > After running VOIDOO, you will get the log file with cavity volume > information. It has the average volume and the sigma volume information, > but along with that If you look at the end of the log file, you will find > the "Cavity volume on plot grid (A3)" provided separately. This is the > volume you report. > > Example:- in the output log file, scroll down to find the following line > in the end: > > Nr voxels/Voxel volume/Cavity volume on plot grid (A3) 860 0.3429999 > 294.980 > > and the cavity volume you report in this case is 294.980. > > Hope this helps. > > Manish > > > > > > > Hello all > > > > I am comparing the probe-occupied volumes of a protein cavity with and > without several ligands. Which cavity volume is used for the > comparisons? > > > > I found an FAQ link: > > http://www.imsb.au.dk/~mok/o/ofaq/Q.507.html<http://www.imsb.au.dk/%7Emok/o/ofaq/Q.507.html> > <http://www.imsb.au.dk/%7Emok/o/ofaq/Q.507.html> > > > > Q.507 - Which VOIDOO cavity volume should I quote ? *Category: S.507 - > cavity voidoo * > > > > The question: "Should I use the average cavity volume, or the last > calculated one ? Sometimes those values are not very stable." > > > > If the cavity volumes fluctuate rather wildly: > > > > 1. start with a finer grid (e.g., 0.7 instead of 1 A, or 0.5 instead > of > > 0.7 A) > > 2. use a slightly larger probe radius > > 3. repeat the calculation N times (e.g., N=10) with randomly oriented > copies of your molecule & average those (see the manual and the > paper) > > > > > > However, the reply does not indicate which volume to report. > > > > When the program runs, I see a summary that looks thus: > > > > Summary : > > Nr of cavities found : ( 1) > > Nr of original grid points in cavities : ( 506) > > Total cavity volume (A3) : ( 3.387E+02) > > > > This is the last calculated volume with the finest grid size. However, > this > > summary does not appear in the log file that VOIDOO writes out. > > > > So, which volume should be used? > > > > A. Run VOIDOO for, say 25 cycles to convergence for 10 different random > orientations, and average the final converged volumes (volumes with the > finest grid size) for all. > > > > or > > > > B. Run VOIDOO for 10 cycles for 10 different random orientations, and > average the "average volume for all grid sizes" reported in the log file > for > > 10 different orientations regardless of convergence. > > > > or > > > > C. Run VOIDOO till volumes converge for 10 different random > orientations, > > and average the "average volume for all grid sizes" reported in the log > file > > for 10 different orientations. > > > > I am rooting for A. This seems to make most sense. But why then does the > log > > file not give this value separately although it gives average volume for > all > > grid sizes and standard deviation? I understand that this tells us how > sensitive the volume calculation is to grid size. Is that the only > reason > > these numbers are listed? > > > > Any input will be appreciated! > > > > Thanks, > > Sangeetha. > > > > > > > > >
