From: Tran, Tran (
Date: Tue Oct 04 2016 - 11:12:15 CDT

Thank you Ashar and John!

From: John Stone <>
Sent: Monday, October 3, 2016 5:02:47 PM
To: Ashar Malik
Cc: Tran, Tran;
Subject: Re: vmd-l: Alignment and RMSD calculation

  A quick note: A future rev of VMD will include new commands that will allow
calculation of RMSDs without the need to (re)align them first. I have written
the necessary code to do this but the scripting interfaces are not yet
finalized and will not be exposed until sometime after VMD 1.9.3 is
complete. The new script commands will also allow efficient use of
multi-core CPUs and GPUs for going RMSD calculations for trajectories,
and for clustering analyses of trajectories, and this is why they are
still an ongoing development activity at the moment. That said, for
the time being some simple scripting can do the necessary alignments, or
you can have one of the GUI plugins do it for you.

  John Stone

On Wed, Sep 28, 2016 at 03:46:17PM +1300, Ashar Malik wrote:
> Hi,A
> not sure about the visualization file - butA
> measure fit does not do anything to the coordinates. It computes a
> transformation matrix which has to be applied to the selection something
> like:
> $sel move <transformation mx>
> now the coordinates have been updated.A
> "First,A A the command "measure fit" just align two molecule at a single
> frame, so when I change to the next frame, I need to realign them."
> as to this - I don't exactly see a problem in this!!! you will have to
> loop over all frames and process each individually. The process would
> include --A
> loadng frameA
> calculating the matrixA
> moving the selection using the matrixA
> calculating the RMSD
> I am not sure a way exists where you would not have to align per frame --
> but you could wait for someone else to add to this answer.
> Best,
> /A
> On Wed, Sep 28, 2016 at 2:18 PM, Tran, Tran <[1]> wrote:
> Hi VMD users,
> I'm currently working on two insulin molecules, one from simulations and
> other from x-ray. I have 8000 frames of the simulations one and 1 frame
> of the x-ray.A I want to set the x-ray as reference,A align them while
> running through all 8000 frames ofA the simulations molecule. I used the
> command "measure fit,"A but it created some problems. First,A A the
> command "measure fit" just align two molecule at a single frame, so when
> I change to the next frame, I need to realign them. Secondly, after
> aligning the two molecules, I saved it at a visualization file, however,
> they dont remainA aligning when I reopen the file.A
> Do you know any tools that can help with molecule alignmentA and
> comparing the differences between them?
> Thank you so much!!
> -tranA A A
> --
> Best,
> /A
> References
> Visible links
> 1.

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