• ## Outreach

From: Xiang Gao (xianggao3064_at_gmail.com)
Date: Tue Oct 19 2021 - 02:33:01 CDT

Hi Josh,

can indeed draw triangles among the selected atoms. While the problem is I
have multiple rings that the atoms are not in the right order. So I am
thinking I need to first sort the atoms in the rings, then prepare a script
that generates all triangles in the way you suggest. Hope this will work.

Best,

Xiang

On Tue, Oct 19, 2021 at 3:23 AM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> 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.
>
>
>
> -Josh
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Xiang Gao <
> xianggao3064_at_gmail.com>
> *Date: *Monday, October 18, 2021 at 7:12 PM
> *To: *John Stone <johns_at_ks.uiuc.edu>, Xiang Gao <xianggao3064_at_gmail.com>,
> "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *Subject: *Re: vmd-l: Coloring rings with paperchain
>
>
>
> 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
>
> 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
> <https://urldefense.com/v3/__http:/www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21475.html__;!!HXCxUKc!mIY5PxVs5RK2t2hD6T3EGw5DQwgACjxDpqaVOzfJmWpEc7z53-TNSdQpQVRX-5E\$>.
> By
> > assigningÂ differentÂ beta field valuesÂ 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 withÂ this.
> > Thanks veryÂ much inÂ advance.
> > Best,
> > Xiang
> >
> > References
> >
> > 1. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21475.html
> <https://urldefense.com/v3/__http:/www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21475.html__;!!HXCxUKc!mIY5PxVs5RK2t2hD6T3EGw5DQwgACjxDpqaVOzfJmWpEc7z53-TNSdQpQVRX-5E\$>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science