Re: [Jmol-users] Molecular view (CIF)
Simon,
Here's what I've used. It obviously only works for molecular systems and
can be somewhat slow for very large molecules/unit cells. Bob can probably
figure out a more efficient way to do this, but it works for me. In these
examples I've deleted any molecules that I don't want to see - you may want
to just hide/display molecules instead.
(1) I think this is equivalent to what Bob had suggested before - similar to
Mercury's "include atoms in molecules where *Any* atom fits".
load xxx.cif {333 777 1}; delete not within(molecule, unitcell);
(2) Or (more complicated) - I think this is similar to Mercury's "include
atoms in molecules whose *Centroids* fit".
load xxx.cif {333 777 1};
delete not within(molecule, unitcell);
n = getProperty("moleculeInfo").size;
for (var i=1; i<=n; i++)
{
select molecule=i;
if (({selected}.fx < -0.001) || ({selected}.fx > 1.001) ||
({selected}.fy < -0.001) || ({selected}.fy > 1.001) || ({selected}.fz <
-0.001) || ({selected}.fz > 1.001))
{ hide (hidden || {selected}); }
};
delete hidden;
Dean
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Re: [Jmol-users] 12.1.51_dev problem
Plenty of things wrong with 12.1.51_dev. I've done a lot of changes there, and I'm still working out the bugs. I wasn't able to use my VPN to update files from the Gordon Conference, so that's gotten a bit behind. I'll do an upload, and we can check it out. I'm not seeing the problem at http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm so maybe that's all it was. On Sat, Jul 16, 2011 at 8:13 AM, Otis Rothenberger wrote: > Bob, > > I think there is a modelkit mode bug (break) on 12.1.51_dev dated > 7/6/2011. Your new.htm page is running 12.1.51_dev dated 6/17/2011, and > I don't see the problem there. > > Go to: > > > http://chemistry.illinoisstate.edu/osrothen/web_molecules/script_page_large.aspx > > This is running 12.1.51_dev dated 7/6/2011. To get into Jmol native > modelkit mode in a way that bypasses all of my code, click the Molecular > Editor link and then click the intro link. This will put you in native > modelkit mode and turn off all of my post model edit processing. > > If you replace any H in 2-chlorobutane with C, you will see the problem. > Correct hydrogens also has a related problem. > > Otis > > -- > Otis Rothenberger > chemagic.com > > > > > > -- > AppSumo Presents a FREE Video for the SourceForge Community by Eric > Ries, the creator of the Lean Startup Methodology on "Lean Startup > Secrets Revealed." This video shows you how to validate your ideas, > optimize your ideas and identify your business strategy. > http://p.sf.net/sfu/appsumosfdev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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 -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on "Lean Startup Secrets Revealed." This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Molecular view (CIF)
Rich,
You won't be able to reproduce the exact number of molecules shown in
Mercury, especially with this particular model, which has atoms spread out
over a very large number of unit cells. Options, particularly with that
upgrade I pointed to, not at all with 12.0, and not with the currently
released version of 12.1, either. You need 12.1.51.
1) load xxx.cif
That loads a nice molecular version.
2) load xxx.cif {333 777 1}; display within(molecule, within(cell=555))
That's pretty close. At least it is a 2:1 pairing. I don't know exactly how
Mercury is programmed to display that particular set of models. Maybe you
can tell me!
For reference,
load xxx.cif {555 555 0}
gives you the actual operations, without any modification. The problem with
this file is that the triclinic crystal symmetry produces two very highly
separated and fragmented pieces.
load xxx.cif packed
shows you what is really in the unit cell, but it isn't pretty!
Bob
--
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
--
AppSumo Presents a FREE Video for the SourceForge Community by Eric
Ries, the creator of the Lean Startup Methodology on "Lean Startup
Secrets Revealed." This video shows you how to validate your ideas,
optimize your ideas and identify your business strategy.
http://p.sf.net/sfu/appsumosfdev2dev___
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