From: John Stone (
Date: Mon Oct 18 2021 - 17:05:36 CDT

  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,┬
> 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.

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