VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Wed Nov 06 2024 - 10:22:11 CST

Hi Rajahmundry,
1 - In the objects browser, *Vol* means how many *volume* files you've
loaded.
Gaussian .cube or APBS .dx files are examples of volume files.

2 - The coordination number is the number of atoms, molecules or ions
bonded to a given atom.
*IF* you're comfortable with the automatic bond detection from VMD all you
need to do is to "getbonds".
Review the script below, you may use the VMD Terminal to run it.

Friendly,
Diego.

# Load a ultra-high resolution PDB :)
mol new 4eic

# Create a selection for an Iron (FE) atom. [1]
set sel [atomselect top "index 689"]

# Print the bond list
set bondlist [$sel getbonds]
puts "Bonds: $bondlist"

# Print how many bonds for my selection? [2]
puts "Number of Bonds: [llength {*}$bondlist]"

# Print the bond orders
set bondorders [$sel getbondorders]
puts "Bond orders: $bondorders"

[1] Learn more about the atomselections and getting attributes from
selections
    https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/ug/node122.html

[2] Why am I using {*}
    https://urldefense.com/v3/__https://wiki.tcl-lang.org/page/*7B*2A*7D__;JSUl!!DZ3fjg!8PM0q_qkKBAWQAWeNFTBQ_S_nduHiKTnCLevTrfeka08Wti2cAl37FrqyOa7MZcxfvwerQ04rJKLrQABCXpj$

On Mon, Nov 4, 2024 at 6:30 PM Rajahmundry Ganesh Kumar ch20d408 <
ch20d408_at_smail.iitm.ac.in> wrote:

>
>
> 1. While calculating g(r), how bulk volume is incorporated in it ? (as
> volume shows “0” )
> [image: image]
>
> Is there any source of how g(r) is calculated in VMD ?
>
> 2.How to calculate running coordination number n(r) from VMD ?
> (i.e n(r) vs r)
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu