VMD-L Mailing List

From: Xiang Gao (xianggao3064_at_gmail.com)
Date: Mon Oct 18 2021 - 17:24:08 CDT

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?

Best,

Xiang

On Tue, Oct 19, 2021 at 01:05 John Stone <johns_at_ks.uiuc.edu> wrote:

> 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
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> 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/
>