VMD-L Mailing List

From: Vahdati N. (nadiav_at_soton.ac.uk)
Date: Wed Jun 18 2008 - 10:26:37 CDT

Dear VMD users,

I have understood from previous communications that the extend to which structure can be pulled along each eigenvector can be edited by modifying the range in the ied.py and that for large structures one could extend that range to something in the thousands.

>line 95 of ied.py (version 2.02):
> self.prjLim = [(-50,50) for v in transpose(self.prj)]

My question is how would one assess what range to use for a particular size of structure and any logical meaning of a frame at each point, pulled along on the eigenvector bar. When looking at protein modes, the structure can become quite distorted along each mode, but how can I assess when to stop or that I have pulled the structure enough along the mode. Visual inspection can indicate when bond lengths are distorted too unrealistically but this is not a robust measure.

The coordinates are projected on each eigenvector but what is the relationship between the 'range' set in the code and what we see on the eigenvector bar?

I would appreciate any comments on this.

Thank you very much in advance for your help.

Kind regards,

Nadia

*****************
Nadia Vahdati
Prof. J. W. Essex group
University of Southampton
Southampton SO17 1BJ
UK.