VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 18 2021 - 17:05:36 CDT

Hi,
  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.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

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]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21475.html. 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. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21475.html 

-- 
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/