From: Vermaas, Josh (
Date: Mon Oct 18 2021 - 19:23:39 CDT

Hi Xiang,

If I had to do it, I’d use VMD graphics primitives to fill in the triangles within the ring, which would be whatever color you want. This would be a bit of a pain to script up, depending on what your topology looks like. For a sugar like glucose, where all the atoms are in the right order, you’d do something like this:

set ringsel [atomselect top “resname BGLC and name C1 C2 C3 C4 C5 O5”]
set ringxyz [$ringsel get {x y z}]
graphics top triangle [lindex $ringxyz 5] [lindex $ringxyz 0] [lindex $ringxyz 1]
graphics top triangle [lindex $ringxyz 5] [lindex $ringxyz 2] [lindex $ringxyz 1]
graphics top triangle [lindex $ringxyz 4] [lindex $ringxyz 2] [lindex $ringxyz 5]
graphics top triangle [lindex $ringxyz 4] [lindex $ringxyz 2] [lindex $ringxyz 3]

I *think* I got the triangles right if your sugar is in a chair conformation, since you basically need to turn the 6 membered ring into 4 triangles.


From: <> on behalf of Xiang Gao <>
Date: Monday, October 18, 2021 at 7:12 PM
To: John Stone <>, Xiang Gao <>, "" <>
Subject: Re: vmd-l: Coloring rings with paperchain

Thanks John for your prompt and detailed reply. I would like to ask if you have any idea if there is an alternative way to achieve the effect like paperchain while the colors can be changed in VMD, or using other tools like photoshop?



On Tue, Oct 19, 2021 at 01:05 John Stone <<>> wrote:
  The Paperchain representation currently uses a hard-coded coloring
scheme that maps ring pucker to color. Paperchain uses Hill-Reilly
Pucker Parameters and converts them to a ring color. At present this
supercedes the user-selected coloring mode. This is a bit of an
inconsistent behavior with respect to the way the rest of the
graphical representations work, so I understand the confusion, but
since it is a very special purpose representation that is
really only intended for carbohydrates, this seemed to be a reasonable
approach when it was developed. I had expected that much more development
was going to take place (this was a collaborative project) however
funding for such work is sometimes difficult to maintain.

I feel it will require a little further collaboration with expertise in
carbohydrates and other multi-branched structures to make further
development progress. My recollection is that there are a few areas
where Paperchain could be improved, in addition to what you've asked about.

  John Stone<>

On Tue, Oct 19, 2021 at 12:47:56AM +0300, Xiang Gao wrote:
> Hi,Â
> I am trying to color the 5-rings and 7-rings in my system with different
> colors using paperchain. I tried to follow the way suggested in a previous
> email
> [1]$>. By
> assigning different beta field values to the selected 5-rings and
> 7-rings, I can get the different colors with many drawing method such as
> VMD, CPK and etc. Unfortunately, the coloring does not change with
> paperchain. I would like to know if anyone can help with this.
> Thanks very much in advance.
> Best,
> Xiang
> References
> Visible links
> 1.$>

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science <*Institute*for*Advanced*Science*?entry=gmail&source=g__;KysrKys!!DZ3fjg!umpml7pqhqoLnk7NOVZCRT4l5zZbWuTwnqq0NEGseMQ9OiLd0XMLSTzf-yjrkoNU0w$> and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801$> Phone: 217-244-3349$>