From: Axel Kohlmeyer (
Date: Tue Jun 28 2011 - 09:53:26 CDT

On Mon, Jun 27, 2011 at 3:57 PM, <> wrote:
>  Hello
> Please I need your help. I use tcl . I want to calculate rmsd for each aa 5

please, i need some help, too. ;)

the following could have been written in any language
and i would not have understood it. in order to get
help, you have to try and describe your problem in a
way that somebody that has no clue of what you are
trying to do, can understand it. you seem to be skipping
over too many (non-obvious) details and are using abbreviations
or "slang", so that it is very hard to follow what you are asking.

i am certain that if you would simplify your question,
somebody may be able to help you.


> amstrong this to the groove of mhc molecules, I am using to calculate the
> rmsd 6 mhc molecules overlapping, but when i do the selection of the aa to
> calculate the rmsd,"chain A and sidechain and name CB and same residue as
> (within 5.0 of chain C)" tells me that the selection must have the same
> number of atoms, I was reading the user guide and can not find how to select
> the same aa, eliminating those that do not match without putting in the
> script the resid.Can someone please help me and tell me how I select these
> aa to be the same in the 6 molecules.
> thank you very much
> regards,
> Yaima
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> Infomed:

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.