View source for Modevectors

===DESCRIPTION=== 
[[Image:Modevectors.png|right|thumb|250px|Example showing modevectors in action.  (See Examples below).]]

'''modevectors.py''' is a PyMol script that was originally written to visualize results obtained from Normal Mode Analysis (NMA) by drawing arrows or vectors from a starting structure to a final structure.  However, this script can be used to visualize the direction of motion between two specified states (e.g. targeted MD, comparing open and closed structures, etc).  The strength of this script is that the arrows are highly customizable with numerous options to choose from (see script below).  It is important to note that the two states MUST be identical except for the X, Y, and Z coordinates.  That is, you cannot draw vectors between homologous structures.  The default settings sets the background to white and displays the arrows along with the first object frame (in cartoon representation).


Note: Ray tracing these CGO arrows appears to be a memory intensive process so please save a session before ray tracing and use "pymol -qc" where necessary.  If anybody can come up with a method to improve this please e-mail me (see address in script).

Update: A new way of drawing the arrows has been implemented for PyMOL v.1.1 and has been updated in this code (which automatically detects the version that you are using).  The new method uses the built in cone primitive rather than concentric circles decreasing in size.  Thus, the new method is much less memory intensive and is a significant improvement over the old method.  Additionally, you may want to turn off [[ray shadow]] depending on the [[scene]] that you are viewing as shadows can be confusing to others when seen in publications.