VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Wed Feb 08 2017 - 14:45:52 CST

Hi Josh,

thank you! Yes, this is the sort of image I am trying to make. Just wanted
to make sure there is no ready-made solution for this, especially within
VMD.

Olga

On Wed, Feb 8, 2017 at 3:28 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Olga,
>
> If I understand you correctly, you want to do something similar to the
> abstract image for 10.1021/jp4089113, with a PMF put on top of a molecular
> image? Vector graphics editors inkscape (free) or Illustrator (definitely
> not free) combined with gimp/photoshop are the two programs that come to
> mind for me, since they both can import the vector postscript files that
> xmgrace exports natively, as well as deal with placing molecular images
> saved in a variety of formats. You could also use a variety of python
> libraries (pillow or numpy+matplotlib) to do the image manipulation
> programmatically.
>
> -Josh
>
> On 02/08/2017 12:11 PM, Olya Kravchenko wrote:
> Hi all,
>
> I am trying to come up with a better way to visualize my PMF data (with
> distance as reaction coordinate) and I wanted to overlap the plot with the
> projection image of the channel. Apart from doing it in word/photoshop/gimp
> and/or presenting them side by side, does anyone know if there a software
> that maybe was meant especially for this or similar purpose? Something
> where I could combine the protein image and, say, xmgrace or gnuplot
> results?
>
> Google search was unsuccessful, but maybe I am missing something obvious.
>
> Thanks in advance!
>
> Olga
>
>