VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 14 2016 - 15:36:04 CST
Please CC VMD-L on replies so that others can read and learn from
resolutions from questions like yours.
There are a number of existing plotting scripts and plugins that will
do the kinds of display that you seem to be looking for. Here are several
worth evaluating that are already built-into VMD:
I know of a few custom plotting scripts people have written that
have the same sort of interactive selection and linkage to the
trajectory like ramaplot does, but I don't think they are posted
on the web at this moment. Have a look at the items above
and see if those look like something you could work with or modify
to do what you want.
On Thu, Jan 14, 2016 at 05:38:28PM +0100, Matthias Ernst wrote:
> Hi John,
> I was mainly thinking about energy landscapes for a (long) MD
> simulation, as e.g. generated by PCA.
> Usually, we use 1D or 2D projections and it would be really nice if
> these could be shown in a similar way like the Ramachandran plot
> analysis tool does.
> Another 1D example would be energy during an energy minimization (good
> old molden does it nicely for QM simulations) or temperature. pressure,
> radius of guration,... during an MD or similar data, where it would be
> instructive to see both the structure and the data point in the
> corresponding curve at the same time.
> Should I provide some sample input for my examples?
> On 01/13/2016 07:05 PM, John Stone wrote:
> > Hi,
> > With a little bit of scripting, it is certainly possible to
> > load arbitrary 1-D or 2-D data and associate it with MD trajectory
> > frames and have the two linked in various ways. Do you have a
> > particular example of the sort of information that you're interested
> > in loading and interacting with?
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> > On Fri, Jan 08, 2016 at 07:55:49PM +0100, Matthias Ernst wrote:
> >> Hi,
> >> first of all, thanks for the nice software VMD which I really enjoy
> >> working with!
> >> I have a question. When I load an MD trajectory of a protein and
> >> calculate the Ramachandran plot, I can scroll through the trajectory and
> >> the current value in x/y is automatically shown in the plot. On the
> >> other hand, if I click on a point, the corresponding frame is chosen.
> >> Is it also possible to load external data (in 1D or 2D) and show it in
> >> the same way (highlighted when scrolling, possibly even going to the
> >> timeframe when selecting)?
> >> Thank you very much,
> >> Matthias Ernst
> >> --
> >> Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611
> Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/