From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Tue Mar 26 2013 - 17:38:11 CDT

Thanks,

The problem is that one HEME residue has hydrogens and the other doesn't.
I guess I can remove the hydrogens or say something like "resname HEME and
not hydrogens"?

-Yarrow

> Hi,
> As the error message indicates, the number of atoms that results from
> the in the alignment selection text must be exactly the same for the two
structures (or frames) you want to align. If you're getting differing
numbers of atoms from the same selection text, then you need to choose
an atom selection that will result in the same atom count, and more
generally
> the same atoms (matching parts of related structures) between the two
molecules.
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Tue, Mar 26, 2013 at 12:19:48PM -0700, Yarrow Madrona wrote:
>> Hi,
>> I know this is a basic question but I am having trouble alining two
very
>> similar molecules (98% seq homology) based on a heme selection. Each time,
>> I get the following complaint,
>> measure fit: selections must have the same number of atoms
>> A similar result happens when I try to use the RMSD caclulator
>> extension.
>> Any help would be appreciated. Thank you.
>> --
>> Yarrow Madrona
>> Graduate Student
>> Molecular Biology and Biochemistry Dept.
>> University of California, Irvine
>> Natural Sciences I, Rm 2403
>> Irvine, CA 92697
>> --
>> Yarrow Madrona
>> Graduate Student
>> Molecular Biology and Biochemistry Dept.
>> University of California, Irvine
>> Natural Sciences I, Rm 2403
>> Irvine, CA 92697
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/

-- 
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697