VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 24 2002 - 15:30:25 CDT

Dear Tran,
  At present there is no way to perform atom selections between multiple
molecules in VMD. The easiest way to get around this problem would
be to concatenate your two PDB structures into a single PDB file.
(removing the "END" record so it gets read as a single structure..)
One could write C code, a Tcl script or Python to do within type
distance based atom selections, but there is not a clean way to do this
within VMD's existing framework. If anyone else has ideas, please
feel free to chime in, otherwise I think concatenating the structures
may be the easiest means of doing this. It'll work as then VMD will
think of it as a single "molecule".

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 24, 2002 at 10:23:46AM +1000, Tran Trung Tran wrote:
> Hello
>
> I have two molecules from two different pdb files, and I wish to find
> all the atoms in molecule A that are within 5 Angstrom of molecule B.
> Please advice me how to do this.
>
> I understand the usage of the command “within”, for example
> atomselect 1 “within 5 of resname LYR”
>
> However, I do not know how to use the command “within” when two
> different molecules are involved.
>
> Thanks in advance
>
> Tran Trung Tran
> 

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