VMD-L Mailing List

From: Alexander Balaeff (abalaeff_at_chem.duke.edu)
Date: Fri Jan 20 2012 - 13:59:55 CST

On Thu, 19 Jan 2012, Axel Kohlmeyer wrote:
> If you don't like VMD's choices you can always write a little script
> that changes it or use a file format that does contain the radius
> information in a way that VMD supports reading it.

Along these lines, let me share a little TcL code below that sets
the atomic van der Waals radii based on the value in the Q
(occupancy) column of the PDB file. I use that as an ad hoc
method to illustrate the average electron density on an atom
during an MD simulation. Load a PDB file that contains the van
der Waals radii in the Q column, source in the TcL code, click
Control-v, voila. Note that the van der Waals radii are actually
recalculated by scaling the numbers in the Q column (cf. the
procedure QtoR) -- change that behavior as you see fit.

Best,

Alexander.

--------------------------------------------------------------

proc QtoR {{nmol top}} {

   set all [atomselect $nmol "all"]
   set rzero [$all get radius]
   set newR ""; foreach r $rzero q [$all get occupancy] { lappend newR [expr sqrt($r*$q)/5] }; $all set radius $newR

}

proc VDW_QtoR {} {

   QtoR

   mol representation {VDW 1.0 16}
   mol color {Name}
   mol selection {all}
   mol addrep top

}

user add key Control-v VDW_QtoR

--------------------------------------------------------------

On Thu, 19 Jan 2012, Axel Kohlmeyer wrote:

> On Jan 19, 2012, at 10:03 PM, "Zumot, Elia Nabil" <enz1_at_pitt.edu> wrote:
>
>> Dear VMDers,
>>
>> Any reason why VMD shows sodium ions to be bigger than chloride when it should be the other way around?
>>
>> In crystals the radius of Na+ is 0.095 nm and that of Cl- 0.181 nm.
>>
>
> That is because VMD cannot tell the difference between an element and
> an ion or a chlorine or chloride and a carbon.
>
> If you don't like VMD's choices you can always write a little script
> that changes it or use a file format that does contain the radius
> information in a way that VMD supports reading it.
>
> VMD is very deliberately a very dumb and ignorant software that relies
> on you to provide it with the proper information. It does not even try
> to be smart (for the most part, that is).
>
> Axel
>
>
>
>>
>> Thanks
>>
>> Elia Zomot
>>
>>
>>
>> Elia Zomot, PhD
>> Computational and Systems Biology Department
>> School of Medicine, University of Pittsburgh
>> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
>> Voice: 412 624 8699 - Fax: 412 648 3163
>> enz1_at_pitt.edu
>

========================================================
                Dr. Alexander Balaeff
  Department of Chemistry Phone: (919) 660-1634
  Duke University, Box 90349 FAX: (919) 660-1605
  Durham, NC 27708-0349 E-mail: abalaeff_at_duke.edu
========================================================