From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 01 2013 - 02:58:10 CDT

please always respond to the mailing list, to that people get to see
the replies and can look up the resolution in the future, if they run
into the same issue. thanks.

On Tue, Oct 1, 2013 at 9:47 AM, CHEN, Chi <cchenae_at_ust.hk> wrote:
> Dear Axel,
> Thanks for your quick response.
> I used VESTA to produce the figure I described and succeeded.
> I was just wondering if there is a way to do that in VMD, because I saw in
> one paper they used VMD.
> http://pubs.rsc.org/en/content/articlehtml/2010/cp/c001809k

> I thought it was high level vmd technique. That's why I ask.

this is a much simpler issue and that is indeed possible with VMD plus
some postprocessing. i would create that kind of picture through
"greenscreening", i.e. you create two images from the same setup. the
first you create with the regular isosurface. in the second you have
solid box walls and colormap the volumetric data set on it. in the
color scale, you use one specific color (e.g. purple, cyan, magenta or
white or gray) that is not otherwise present for the part of the box
surface, that you want to cut away. you render both images and load
them into gimp or photoshop and then do a "select-by-color" on the
second image, cut away the unwanted part and overlay this image to the
first. voila!

axel.

> Thank you very much again.
>
> Chi
>
>
> -----邮件原件-----
> 发件人: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> 发送时间: 2013年10月1日 15:21
> 收件人: CHEN, Chi
> 抄送: vmd-l_at_ks.uiuc.edu
> 主题: Re: vmd-l: How to show section contour of volumetric data
>
> On Tue, Oct 1, 2013 at 3:57 AM, CHEN, Chi <cchenae_at_ust.hk> wrote:
>> Dear All,
>> Thanks for taking your time reading this.
>> I have a volumetric density data generated by volmap plugin. I know
>> how to show the isosurface, but only the isosurface is not very pleasing,
> since the cross section of the volumetric data is not shown, which makes
> the isosurface a little weird. By cross section, i mean for example if we
> use a clip plane, we can cut the isosurface, creating a hollow cross
> section. There is a volumeslice method which does almost what I want, but it
> shows the whole slice plane instead of the part it intersects with the
> isosurface.
>
> there actually is no real question here, but it seems what you want is to
> have an option to "close" an isosurface, when you place a cutting plane
> through it (the colorization is independent of that).
>
> that option does not exist. to have that, you need to look into using a
> visualization tool that is more grid data oriented (and less molecular),
> e.g. paraview, visit, opendx, etc.
>
> axel.
>
>
>>
>> I hope this is clear.
>>
>> Thanks
>>
>> Chi
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International
> Centre for Theoretical Physics, Trieste. Italy.
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.