[ccp4bb] VOIDOO average volume report

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

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Subject: VOIDOO average volume report
From: Sangeetha Vedula sangeetha {- dot -} bb {- at -} GMAIL {- dot -} COM
Date: 2008-08-20

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

Previous message:
Subject: Re: Refmac problems on Mac OS X Leopard
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-08-20

Next message:
Subject: Lower completeness, decent R factors, but low B factor...
From: James Pauff pauffjm {- at -} YAHOO {- dot -} COM
Date: 2008-08-20