On Thu, 26 Oct 2006; Subject: Re: ask about 3V program
- I'm a student who is interesting in the program for calculation of molecule volume. I'm working on cytochrome P450 monooxygenase, and trying to classify them based on their shape of access channels. Yesterday I found your 3V program. It's great! But there's a bit problem that I couldn't find any user guide (where are output results, unit or principal documentation of your method. The results which I received from my 3V compiled program and from 3V website are difference even in the same structure. It will be pleasure if you can help me explain on above unclear points? Thank you in advance.
- I currently don't have much documentation on the program, but I am writing my dissertation on it now. I have some figures on how it works and I could send those to you.
  
  All units are in Angstroms (1 A = 0.1 nm), the variation between the web and the program is likely related to the grid size, the web features grid size of 0.75, 1.0, and 2.0 but the prgram defaults to 0.5 A. The smaller the grid the more accurate.
  
  To get output, the volume, etc is printed to STDOUT, but to get volumetric results you need to type "-o pdbfile" or "-e ezdfile" the ezd file can then be converted to whatever using the program MAPMAN, I typically convert it to CCP4 for viewing in PyMOL or Chimera. The website automates this whole process with some scripts.
  
  I would be happy to help you through any further questions that you may have.
  
  neil
On Mon, 30 Oct 2006
- Now i know how to control the Volume.exe. But with Cavities, Tunnel.exe and other executed files in bin directory, I have no idea how to run them. Could you show me how their syntaxes?
- For all the programs type -h to get syntax list. examples:
  
  >./Volume.exe -h
```
./Volume.exe -i file -g gridspacing -p probe_rad -e EZD_outfile -o PDB_outfile
```
  >./Solvent.exe -h
```
./Solvent.exe -i file -s sm_probe_rad -b big_probe_rad
        -t trim_probe_rad -g grid spacing -e EZD outfile -o PDB outfile
```
  >./Channel.exe -h
```
./Channel.exe -i file -b big_probe -s small_probe
        -t trim probe -x x-coord -y y-coord -z z-coord
        -e EZD outfile -o PDB outfile -g gridspace
```
  Channel is like Solvent, but select a particular channel at point x,y,z
  
  Tunnel.exe is "worthless" unless you are studying the ribosome
  
  Eveything has a default value, except the input file.
  
  neil
On Mon, 4 Jun 2007