Re: atom selection error

From: Brian Radak (
Date: Fri Dec 08 2017 - 10:41:57 CST

This really isn't enough information to understand what the problem is. Can
you give sequential steps of *exactly *what you are doing? What files did
you load? Are you using the GUI or terminal commands? What is your
selection string and how are you communicating it to VMD?

If I had to guess, I would say you probably have a bad selection string. A
good way to test your selection would be to try making a representation for
just those atoms.


On Fri, Dec 8, 2017 at 9:22 AM, Shahee Islam <>

> Thank you so much for your reply.i want to calculate the rmsd of
> backbone.And Still when I try to recentering the coarse grained proteins
> ,the atoms are not selecting.
> On Dec 8, 2017 7:29 PM, "Peter Freddolino" <> wrote:
>> You would need to send much more information on how you're trying to
>> calculate the RMSD. My wild guess is that you're looking for alpha carbon
>> or recognizable backbone atoms when none exist.
>> On Fri, Dec 8, 2017 at 3:33 AM, Shahee Islam <>
>> wrote:
>>> Hi,
>>> i have prepared my system according to rbcg tutorial.Now i want to
>>> analyse my system by vmd,but during the analysis(rmsd) atoms are not
>>> selected and also in the time of recentering of proteins.Can anyone please
>>> help me why this is happening.
>>> Also i want to know is there any other method to analyse the coarse
>>> grained system(which is made according to rbcg tutorial).
>>> Thankig you
>>> Shahee Islam
>>> University of calcutta
>>> Department of chemistry

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