VMD-L Mailing List

From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Tue Mar 26 2013 - 20:07:40 CDT

Structures with non-identical sequence can't have the same number of atoms (even at 98% identity).
But the OP wrote he was trying to align based on a heme selection. That should be possible, unless indeed there are different numbers of heteroatoms in the hemes in the structure file. Check the file. I suspect the HETATM records would also need to have the same atom names and/or be present in the same order(!) in the structure file.

You have to understand that the RMSD algorithm requires a list of equivalent atom pairs. Ask yourself whether VMD has all the information it needs to establish such a list. For example, VMD has no inbuilt knowledge of heme topology and nomenclature. And you don't know whether VMD builds the pair-list sequentially per residue (the simple approach), or maps atoms to a template (a more robust approach, that would be required for some legacy PDB files; but requires such templates).

B.

On 2013-03-26, at 5:21 PM, Ishwar Hosamani wrote:

> Hello Yarrow,
>
> This might seem silly and has happened to me before.
> Have you checked the number of atoms in both your structures.
> It is possible that one of your structures is solvated while the other is not.
> Get rid of the water molecules and you should be good to go.
>
> Cheers,
>
> On 2013-03-26, at 1:10 PM, 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
>>
>>
>>
>
>
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