VMD-L Mailing List

From: Nuno Ricardo Loureiro Ferreira (nunolf_at_ci.uc.pt)
Date: Sat Dec 02 2006 - 03:18:05 CST

Hi Jay

You're right, shame on me ;-) The procedure it's not there anymore.
Check: http://www.ks.uiuc.edu/Research/vmd/current/ug/node181.html

About the drawing of lines between the desired c.o.m. of hydrop. residues, you can play with the draw command, check this: http://www.ks.uiuc.edu/Research/vmd/current/ug/node114.html

I just changed a little bit this last procedure, removing the arrow part, this way you will get a cylinder:
proc vmd_draw_cyl {mol start end} {
    set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
    graphics $mol cylinder $start $middle radius 0.15
}The var "start" will be the coordinates of COM of residue X and "end" will be the COM of residue Y.

Cheers,
Nuno
  ----- Original Message -----
  From: gcmc jie
  To: Nuno Ricardo Loureiro Ferreira
  Sent: Friday, December 01, 2006 1:34 AM
  Subject: Re: vmd-l: draw hydrophobic contact

  thank for your hint. Actually, I knew the whole procedure of how to count the hydrophobic contacts using CHARMM scripts.

  My current problem is how to draw the lines between two hydrophobic side chains if they have a contact by using VMD. I am not quite familar with TCL.

  by the way, why I can not find COM script in vmd script libarary.

  Best,

  Jay

  On 11/30/06, Nuno Ricardo Loureiro Ferreira < nunolf_at_ci.uc.pt> wrote:
    HI Jay

    If you are a new user, then you must start from the beginning, by reading the manual.
    I can give you the following tips:

    1- vmd already as built in commands that allows you to select the hydrophobic residues
    2- also has in the scripts libarary (web page) a c.o.m script
    3- the process will be something like this:

        select hydrophobic residues
        determine the com of the side chain of those select residues
        select the pairs of residues which have a distance between their com < 4 angst.

    Sorry if this is to crude, but VMD is a great analysis tool. But for that, you need to give a little of your time. Just start by the tutorials on the web page.
    Nuno
      ----- Original Message -----
      From: gcmc jie
      To: vmd-l_at_ks.uiuc.edu
      Sent: Thursday, November 30, 2006 7:41 PM
      Subject: vmd-l: draw hydrophobic contact

      Hi all,

      I want to indicate the hydrophobic contacts at the interface between two domains. hydrophobic contact is defined when the center of mass of distance between two hydrophobic side chains is less than 4 Å. I would like to draw lines to show these hydrophobic contacts.

      Since I am new to use VMD, I google and search vmd-mail-list, I could not find similar script?
      anybody can give me hint. thanks in advance.

      Jay