VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Sep 27 2016 - 21:46:17 CDT

Hi,

not sure about the visualization file - but

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.

"First, 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 --

loadng frame
calculating the matrix
moving the selection using the matrix
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 <TrTran_at_clarku.edu> 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. I want to set the x-ray as reference, align them while running
> through all 8000 frames of the simulations molecule. I used the command
> "measure fit," but it created some problems. First, 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
> remain aligning when I reopen the file.
>
> Do you know any tools that can help with molecule alignment and comparing
> the differences between them?
>
> Thank you so much!!
>
> -tran
> 

-- 
Best,
/A