VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Tue Jan 13 2015 - 10:36:11 CST

Jian,
I've have a related problem and molefracture complains that my molec is too big...

I thought the ramachandran plot under
"extensions -> analysis -> ramachandran" was interactive ...
meaning you can drag and drop the angle to whatever you like ....
but I checked and it's not.

If you want to rotate around a bond (even a virtual bond) you can use this scriptlet
http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node181.html

Using the following in combination w/ the Rama Plots should allow you to do pretty much what you had in mind
but modify to rotate entire molec. rather than just a side chain
e.g.   set sidechain [atomselect top " residue > 22"]
but this is also tedious.


A more useful example is the following, which rotates the side chain atoms around the CA-CB bond by 10 degrees. 
# get the sidechain atoms (CB and onwards)
set sidechain [atomselect top "sidechain residue 22"]
# get the CA coordinates -- could do next two on one line ...
set CA [atomselect top "name CA and residue 22"]
set CAcoord [lindex [$CA get {x y z}] 0]
# and get the CB coordinates
set CB [atomselect top "name CB and residue 22"]
set CBcoord [lindex [$CB get {x y z}] 0]
# apply a transform of 10 degrees about the given bond axis
$sidechain move [trans bond $CAcoord $CBcoord 10 deg]



On 01/13/2015 08:23 AM, Jian Dai wrote:
Dear VMD developers:
I want to build an alpha helix that has customized parameters, for example, I want the angles between CA, C and N to be 115 instead of 118 degrees (Molefacture default value). 
I can do this manually via the Molefacture molecule builder but it becomes laborious and error-prone when there are lot of such manipulations. How to do it using the command line? I read the source code for Molefacture and find that "resize_angle" is relevant, but I don't know how to select the angle to manipulate by the command and then use resize_angle to change it to a target value.
Any suggestions?
Thank you very much.
Jian