The substructure command is working, just not for Nick. ;) Nick's solution will depend upon whether he is looking for a general solution that does not depend upon knowing the polymer structure or whether he knows what file he is working with. His files are Spartan output, so they come with "HETATM...UNK" for all atoms. I think the select (BRANCH,...) option could work here. For example, something like this worked for me.

function selectMonomer(i)
† var n0 = 12
† var natoms=14
† var nr = 0
† var n1 = n0 + natoms*i
† print "" + n1 + " " + natoms
† select within(branch,@{"atomno=" + n1},@{"atomno=" + (n1 + 1)})† and not within(branch,@{"atomno=" + (n1 + natoms)},@{"atomno=" + (n1 + natoms + 1)})
end function

On second thought, maybe just atom numbers are easier...

2009/5/27 Angel HerrŠez <angel.herraez@uah.es>
> On Tue, May 26, 2009 at 6:10 PM, Nick Greeves <ngreeves@liverpool.ac.uk> wrote:
> † † Thanks Bob, I am trying with PDB but I'm not clear how to specify "residues". I liked the

Nick, apart from specfying aton numbers as Bob says, the other solution is
that you insert residue "names" in the pdb fle. You usually have to give
them too a unique residue number so they are recognized as separate
residues.

Do you have a sample file?

On the other hand, we must find out if the "substructure" command is not
working. You have another choice: to use the "connected" syntax to build
specifications for some residues, but I don't think that will help you in
separating one from the next.


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