VMD-L Mailing List

From: Amit Gupta (amit__at_outlook.in)
Date: Sat Jan 14 2017 - 00:32:03 CST

Thank you for the glow script. (i downloaded from here http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-16090/glowlights.tcl)
it worked perfectly except one issue, It gave error message:
------------------------------------------------------------
Parse Error:
   Encountered a syntax error in file vmdscene.dat
   Expected to find an object or other declaration
   Actually found: E
   Error occured at or prior to file offset 75900, line 2887
   Error position is only approximate, but should be close

I edited line 118, from: seek $fd -11 end, to seek $fd -12 end, and it worked.

Regarding images:
http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/bobjohnson/graphene-nanopore.jpg
and
http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/bobjohnson/graphene-device.jpg

I understand that DNA is newRibbon, what about graphene sheet? I tried giving it as new ribbon but nothing happened.

My problem is, I want to show certain planer molecules like anthracene adsorbed on graphene, hence above representation made most sense, therefore any way to achieve similar effects?
that is having inner enclosed area of a ring of molecules filled wit flat translucent sheet in vmd?

________________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Saturday, January 14, 2017 10:48:08 AM
To: Amit Gupta
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Rendering images like those shown on VMD home page

Amit,

On Sat, Jan 14, 2017 at 04:57:34AM +0000, Amit Gupta wrote:
> Hi, I would like to know if anyone can shed any light on how these two figures were rendered in VMD/Tachyon
>
> 1.
> http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/bobjohnson/graphene-nanopore.jpg

This was drawn using the NewRibbons representation in combination with
the Licorice representation. The PaperChain representation was not used
at all in that figure, so the rest of the questions/comments for 1) below
are not relevant to that image.

> No matter what i do i cannot change color of paperchain in vmd. Similar thing is discussed here :http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21475.html
> however I cannot change color by selecting color type color-id. All my rings are red.

PaperChain is really meant to be used for carbohydrate, not DNA...

> 2.
> http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/afenley/The_Core_of_Eukaryotic_Life.jpg
> the 'glow' that yellow spheres are emitting, is it possible in vmd or
> its very impressive photoshop? If possible, then how to make it in VMD?

While I didn't help make that image, I expect that Prof. Onufriev's
team used the "glowlights" script I had previously made available
on the VMD-L list to make that figure. In essence, the glowlights
script adds extra lights into a VMD scene that can be rendered by Tachyon.
Unlike the normal infinite directional lights in VMD, the glow lights can
be positioned within the molecule, and they can have an arbitrary
set of quadratic distance attenuation coefficients, yielding the very
localized lighting such as is shown in that figure. It is possible
that they did this by hand, editing a Tachyon scene file themselves,
or that they might have used a version of the glowlights script I've
previously made available.

Here is a rendering by some of the people in our Center that used the
glowlights to add extra local lighting in various places, albeit with
some photoshop in a couple of places too:
  http://www.ks.uiuc.edu/Gallery/Science-New/images/transporters-channels/2012-BIposter-MscS-Ramya-1000x800-stamped.jpg

You might also get other ideas from the VMD images produced here as well:
  http://www.ks.uiuc.edu/Gallery/Science-New/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu 

--
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/