VMD-L Mailing List

From: Payne, Christina M (christy.payne_at_uky.edu)
Date: Wed Sep 04 2013 - 12:43:56 CDT

Mish,

You are correct in that if you select the entire ring, $sel get pucker will return six equal values, which is the Cremer-Pople puckering amplitude for the ring. I would suggest selecting a single atom within your hexapyranose.

Dr. Kuttel describes how the paperchain algorithm works in her 2006 J. Molec. Graph. Model. paper, "Techniques for visualization of carbohydrate molecules." The pucker command appears to query only the amplitude, Q, though coloring is achieve by calculating all three parameters. I am not aware of an existing command to query theta and phi directly.

I have previously posted a script to the VMD mailing list to loop over a trajectory to get the CP amplitude (it's mislabeled as hrpucker).
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/18331.html

To get theta and phi, you can modify this script to select each of your six atom coordinates, every frame, and calculate the appropriate pucker parameters. Look into tcl scripting within VMD (in the user guide) to figure out how to use the script and start learning how to modify it for your use.

One final note, it is bad practice to send emails to individuals' email addresses in addition to the mailing list. This mailing list is a resource for everyone, so responses should not be lost to one user. Be patient waiting for responses.

Christy 

--
Christina M. Payne
Assistant Professor of Chemical Engineering
University of Kentucky
159 F. Paul Anderson Tower, Lexington, KY 40506
(859) 257-2902 | Christy.Payne_at_uky.edu
From: mish <smncbr_at_gmail.com<mailto:smncbr_at_gmail.com>>
Date: Wednesday, September 4, 2013 8:49 AM
To: "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>" <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: vmd-l: Puckering Parameters
Dear all,
I am new to Tcl scripting and thus I need some help regarding pucker value calculation in VMD. I want to calculate Cremer-Pople (CP) ring puckering parameters from the AMBER trajectory in VMD. I have all the hexa-pyranoses in the structures.
I am able to select 6 membered rings by > "ringsize 6 from resid 1". I found in the mailing lists "$sel get pucker"  gives the Hill-Reilly ring pucker value (should be one non-zero values for 6-membered rings). When I use "$sel get pucker", it gives 6 values and they all are same(probably one for each atom).  In the article D. Hill & Reilly calculated theta 1, theta 3 and theta 3, three values. But I am surprised that how can a single Hill-Reilly pucker value determine three angles characteristic of the conformations ?
If not hen I want to calculate Cremer-Pople parameters for all the rings and all the frames in trajectory. Cab someone help me if it can be easily done in VMD somehow ? or if it is described in manual somewhere.
Thanks
Mish