This prototype file demonstrates the new "collapsed" idea for polyhedra and the new select connected() idea.

connect and polyhedra

• load NaCl.mol; select *
• polyhedra 6 3.0 (chlorine) to (sodium) collapsed edges;
• connect 3.0 (*)
• polyhedra 6 (chlorine) collapsed edges; color polyhedra yellow
• select *; wireframe off; spacefill off;
• select connected(6); spacefill 0.5;




3. combining with draw objects

• load quartz.mol
• draw line1 150 (atomno=2) (atomno=17)
• spin internal $line1 30
• spin off
• polyhedra 4 (silicon) to (oxygen) collapsed edges
• polyhedra 4;color polyhedra red
• polyhedra edges;
• load P4O10.mol;polyhedra 4 collapsed edges
• draw line2 150 (atomno=2 or atomno=11 or atomno=3) (atomno=13)
• spin internal $line2
• spin off




2. faceCenterOffset for collapsed polyhedra

• load ZNQUKROD.mol;
• select zinc;polyhedra bonds flat edges;
• select zinc;polyhedra bonds collapsed edges;
• select carbon;polyhedra bonds faceCenterOffset 0.4 collapsed edges;
• draw line2 150 (atomno=40) (atomno=35)
• spin internal $line2
• spin off
• load TCBEWREA.mol
• select not nitrogen;polyhedra bonds faceCenterOffset 0.0 collapsed edges
• select not nitrogen;polyhedra bonds faceCenterOffset 0.25 collapsed edges
• select not nitrogen;polyhedra bonds faceCenterOffset 0.5 collapsed edges
• select not nitrogen;polyhedra bonds faceCenterOffset 0.9 collapsed edges
• select not nitrogen;polyhedra bonds faceCenterOffset 1.2 collapsed edges




1. polyhedra extending beyond the unit cell

first we load nine unit cells
• load "y1237.cif" {3 3 3}
we restrict ourselves to just the center cell -- note, these numbers can be fractional
• restrict cell={2 2 2};
we offset the unit cell to the origin of this central cell and display it
• set unitcell {1 1 1};axes off;color unitcell white;center visible;moveto 1.0 -971 195 138 78.9 225;
some connection adjustments first
• connect (copper) (copper) delete;
• connect (yttrium) (*) delete;
now we draw the polyhedra just to what is visible and connected the way we want
• polyhedra bonds (copper and (connected(4) or connected(5)) and visible)
and we hide the bonds. Voila!
• select *;wireframe 0;
finally, if we wish, we can close that final side:
• polyhedra bonds (copper and (connected(4) or connected(5)) and visible) distanceFactor 2.0
fractional offset, same idea:
• load "y1237.cif" {2 2 2};restrict cell={1.5 1.5 1.5};set unitcell {1/2 1/2 1/2};axes off;color unitcell white;center visible;moveto 1.0 -971 195 138 78.9 175;
• connect (copper) (copper) delete;connect (yttrium) (*) delete;
• polyhedra bonds (copper and (connected(4) or connected(5)) and visible)
• select *;wireframe 0;

[appletInfo] [animationInfo] [fileName] [fileHeader] [fileContents]
[atomList] [atomInfo] [bondInfo] [extractModel]
[orientationInfo] [transformInfo] [centerInfo] [boundboxInfo] [zoomInfo]
[modelInfo] [polymerInfo] [chainInfo] [shapeInfo] [stateInfo] [reload THIS orientation]

monitor: atomPicked fileLoaded fileLoadError frameChanged
measurePending measureCompleted measurePicked scriptStarted
scriptEcho scriptStatus scriptError scriptMessage
scriptTerminated userAction viewerRefreshed newOrientation
all none

Decoded: new window