To help us remember what new things there are in Jmol as we develop them, I thought I would start a new page. Ulimately these will be incorporated into the documentation, but for now, here are some sneak peeks into Jmol 10.1. What am I forgetting? As I remember new features or people suggest that I include them, I will.
http://www.stolaf.edu/people/hansonr/jmol/test/10.1/new.htm
The current list of demo scripts for 10.1 includes:
* ### SELECT CONNECTED() ###
* load mol/ZNQUKROD.MOL;
* select connected();color green
* select connected(7);color red
* select connected(zinc);color yellow
* select connected(2,hydrogen);color blue
* select hydrogen and connected(connected(2,hydrogen));color orange
* ### CONNECT ###
* load caffeine.xyz
* connect 1.2 1.26 DOUBLE (carbon) (oxygen)
* connect 1.5 DOUBLE (carbon) (connected(2,nitrogen))
* connect 1.5 DOUBLE (nitrogen and not connected(3))
(connected(1,hydrogen))
* #options for bond type include SINGLE, DOUBLE, TRIPLE, AROMATIC,
and HBOND
* connect 2.0 AROMATIC (carbon) (connected(2,nitrogen))
* connect 2.0 AROMATIC (nitrogen and not connected(3))
(connected(1,hydrogen))
* connect HBOND (oxygen) (oxygen)
* #new hbonds are thin lines
* connect DELETE HBOND
* connect DELETE AROMATIC
* connect 2.0 CREATE AROMATIC (*) (not hydrogen)
* select not (connected(3,hydrogen) or hydrogen);color yellow
* connect MODIFY HBOND
* #modified hbonds take previous bond's diameter
* load mol/NaCl.mol;
* select atomno < 100;connect 3.0
* #atom set can be pre-selected
* select atomno < 100; connect (atomno > 100) 3.0
* #missing one or both atom set implies (selected)
* load mol/NaCl.mol
* connect 3.0 (chlorine) (sodium)
* #only nearby Na-Cl formed
* connect delete (chlorine) (sodium)
* select (chlorine); connect 3.0 (sodium) #same thing
* connect delete (chlorine) (sodium)
* connect 3.0 6.0 hbond (chlorine) (sodium)
* #only distant Na-Cl formed
* connect delete hbonds (chlorine) (sodium)
* ### POLYHEDRA and CONNECT ###
* load mol/NaCl.mol
* connect 3.0 (chlorine) (sodium)
* #this is needed for bonding designation in the polyhedra command
* polyhedra 4,6 (chlorine) collapsed edges; color polyhedra yellow
* #the new "collapsed polyhedra" idea
* polyhedra 6 3.0 (chlorine) to (sodium)
* #only the chlorines that are within 3 Angstroms of exactly 6 sodiums
* select *; wireframe off; spacefill off;
* select connected(6); spacefill 0.5;
* #here we use those connections to provide clickable atoms (for
distance and angle measurement)
* select connected(6); spacefill 0.005;
* #they can be almost inperceptible but still clickable
* load quartz.xyz
* polyhedra 4;color polyhedra red
* #the standard look
* polyhedra edges;
* #edges are a nice touch
* polyhedra (silicon) to (oxygen) collapsed edges
* #the "collapsed" look
* load mol/P4O10.mol
* polyhedra collapsed 4 edges
* load mol/ZNQUKROD.MOL;
* select zinc;polyhedra bonds edges;
* select zinc;polyhedra bonds collapsed edges;
* select carbon;polyhedra faceCenterOffset 0.4 collapsed edges;
* load mol/TCBEWREA.MOL
* polyhedra (*) (*) collapsed edges
* #notice the effect of faceCenterOffset:
* polyhedra (carbon) delete
* polyhedra (carbon) to (nitrogen or hydrogen) collapsed edges
* #if you look closely, not all the planes have been drawn. This
model is quite distorted, so we increase the value of faceNormalMax from
its default value of 30 to 50:
* polyhedra (carbon) to (nitrogen or hydrogen) collapsed edges
faceNormalMax 50
* select not nitrogen;polyhedra faceCenterOffset 0.0 collapsed edges
* #faceCenterOffset of 0 can result in lighting problems
* select not nitrogen;polyhedra faceCenterOffset 0.25 collapsed edges
* select not nitrogen;polyhedra faceCenterOffset 0.5 collapsed edges
* polyhedra delete (*);polyhedra (carbon) TO (nitrogen or carbon or
hydrogen) collapsed edges
* #go wild!...
* polyhedra delete (*);
* polyhedra (technetium) faceCenterOffset -2.2 collapsed edges
* polyhedra delete (*);
* select not nitrogen;polyhedra faceCenterOffset 5.2 collapsed edges
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