From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 26 2017 - 09:49:44 CDT

Make sure that the atom selections you're using for the structures
result in the same count of atoms in all of the structures you're comparing.
Even if they started with the same atom count, the atom selection(s) in use
could potentially result in differences.

Cheers,
  John

On Wed, Jul 26, 2017 at 08:37:36PM +1200, Ashar Malik wrote:
> There is no image attached to you message. Please re-send.
> On Wed, Jul 26, 2017 at 8:08 PM, Afnan Sultan
> <[1]s-afnan.sultan_at_zewailcity.edu.eg> wrote:
>
> Any help?!
> On Sat, Jul 22, 2017 at 4:51 AM, Afnan Sultan
> <[2]s-afnan.sultan_at_zewailcity.edu.eg> wrote:
>
> Hello VMD,
> I am facing a problem with aligning two equal sized molecules using
> RMSD calculator.
> The attached image shows the problem i am facing. The program reads
> the two molecules as equally sized atoms, however, RMSD calculator is
> seeing something else!
> I don't know what i can do. any help?
> Thanks in advance,
> Afnan
>
> --
> Best,
> /A
>
> References
>
> Visible links
> 1. mailto:s-afnan.sultan_at_zewailcity.edu.eg
> 2. mailto:s-afnan.sultan_at_zewailcity.edu.eg

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/