[Chimera-users] display vectors

[Eric Pettersen]

On Oct 11, 2004, at 6:50 AM, Mingfeng Yang wrote:

> I want to show motions of some atoms. Is it possible to draw vectors  
> origin from each atoms in Chimera? Specifically, I like to draw an  
> arrow, originning from each atom, with direction and length to  
> describe the motion.

The answer is yes, though the process is a little involved.  Can I ask  
you in what context you are doing this?  Is it related to an MD  
trajectory?  Perhaps in future releases we could make this easier if we  
know specifically what you want to do and what data you are working  
from.

Anyway, there are two methods I can suggest:  VRML and pseudobonds.   
You can show exactly what you want with VRML, but it may be more  
effort.  Pseudobonds may be easier, but you can’t have arrowheads.

For VRML, you just compose a VRML file using a cylinder and cone for  
each arrow.  The cone is the “arrowhead” and you have the cylinder go  
from the atom to the base of the cone, and have the cone point in the  
right direction.  If you don’t know how to use VRML, this page has a  
spec and examples:   
http://www.web3d.org/x3d/specifications/vrml/ISO_IEC_14772-All/ 
index.html

For pseudobonds, you would make up a fake molecule where the “atoms”  
are at the ends of the vectors you want to show.  If you make a PDB  
file, start it with a TER card and use HETATM records for each atom,  
with a different residue number for each.  This will ensure that  
Chimera won’t connect any of the atoms in the fake molecule.  You can  
then use the PBReader tool (in the Utilities category) to read in the  
pseudobonds to display (including colors and optional labels).  You can  
use the pseudobond panel (under inspectors) to control if the  
pseudobonds are wires or sticks, if they are dashed [wire only], and so  
forth.

Let me know if you need any more help getting started with this.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu