Re: [ccp4bb] VOIDOO average volume report

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Ph.D. studentship in Structure-based Drug Design, University of Luebeck, Germany
From: Holger Steuber steuber {- at -} BIOCHEM {- dot -} UNI-LUEBECK {- dot -} DE
Date: 2008-08-20

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Subject: Re: VOIDOO average volume report
From: mshah {- at -} HWI {- dot -} BUFFALO {- dot -} EDU mshah {- at -} HWI {- dot -} BUFFALO {- dot -} EDU
Date: 2008-08-20

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
>
> 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.
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Re: Coot and OS X Leopard
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-08-20