connect server-side computing with client-side visualization
First of all, I would suggest JSON rather than XML to be used for exchange format, it is much easier to parse JSON at the javascript side.
Then, speaking about the architecture of your app, I think that it is better to write a server web application in Python to generate JSON content on the fly than to modify and serve static files (at least that is how such things are done usually).
So, that gives us three components of your system:

A client app (javascript).
A web application (it does not matter what framework or library you prefer: django, gevent, even Twisted will work fine, as well as some others). What it should do is, firstly, giving the state of the points to the client app when it requests, and, secondly, accepting updates of the points' state from the next app and storing them in a database (or in global variables: that strongly depends on how you run it, a single process gevent app may use variables, when an app running withing a multi-process web server should use a database).
An app performing calculations that periodically publishes the points' state by sending it to the web app, probably as JSON body in a POST request. This one most likely should be a separate app due to the typical environment of the web applications: usually it is a problem to perform background processes in a web app, and, anyway, the way this can be done strongly depends on the environment you run your app in.

Of course, this architecture is based on "server publishes data, clients ask for data" model. That model is simple and easy to implement, and the main problem with it is that the animation may not be as smooth as one may want. Also you are not able to notify clients immediately if some changes require urgent update of client's interface. However, smoothness and immediate client notifications are usually hard to implement when a javascript client runs within a browser.
I am working on a project which would animate points on a plain by certain methods. I intend to compute the movements of the points in python on server-side and to do the visualization on client-side by a javascript library (raphaeljs.com).
First I thought of the following: Running the process(python) and saving the states of the points into an xml file, than load that from javascript and visualize. Now I realized that maybe it would run for infinity thus I would need a realtime data exchange between the visualization part and the computing part.
How would you do that?