Nick, this is done. See http://chemapps.stolaf.edu/jmol/examples-11 and
http://chemapps.stolaf.edu/jmol/examples-11/new.htm
Could be some tweaking to do. For example, right now it loads the molecules
into individual models -- not sure that would be appropriate.
Bob
On Thu, May 28, 2009 at 1:55 PM, Nick Greeves <[email protected]>wrote:
> Hi Bob,I try to know what file I'm working with but I don't always manage
> it!
> Certainly atoms can be picked by hand as Angel suggests or
> semi-automatically as you do.
>
> Would it help if the files themselves had a bit more structure? We are
> testing out Materials Studio which produces .xsd files that look like some
> sort of CML. Jmol can't read them but I wonder if it could read them then
> the structural info looks to me (as a novice) as if it is contained within.
>
> Otherwise MS can output PDB files but they look different again from
> Spartan's effort which you weren't too keen on. We can probably work with
> these.
>
> I enclose a couple of .xsd files for you to see what I mean.
>
> All the best
>
> Nick
>
> --
>
> 3D Organic Animations http://www.chemtube3d.com
>
> Tel: +44 (0)151-794-3506 (3500 secretary)
>
> Re: [Jmol-users] Displaying polymer chains with Jmol
>
> Robert Hanson
> Wed, 27 May 2009 04:42:43 -0700
>
> 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...
>
>
>
>
>
>
>
>
>
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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