VMD-L Mailing List
From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Tue Jan 13 2015 - 10:36:11 CST
- Next message: Axel Kohlmeyer: "Re: Re: FW: atomselection by wildcard and distance exclusion"
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- In reply to: Jian Dai: "Build a customized alpha helix using Molefacture by command"
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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
- Next message: Axel Kohlmeyer: "Re: Re: FW: atomselection by wildcard and distance exclusion"
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