org.jmol.shapebio
Class BioShape
java.lang.Object
org.jmol.shapebio.BioShape
class BioShape
- extends java.lang.Object
Method Summary |
(package private) void |
calcBfactorRange()
|
(package private) short |
calcMeanPositionalDisplacement(int bFactor100)
Calculates the mean positional displacement in milliAngstroms. |
(package private) void |
falsifyMesh(int index,
boolean andNearby)
|
(package private) void |
findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
java.util.BitSet bsNot)
|
(package private) void |
setColix(short colix,
byte pid,
java.util.BitSet bsSelected)
|
private short |
setMad(int groupIndex,
short mad)
|
(package private) void |
setMad(short mad,
java.util.BitSet bsSelected,
float[] values)
|
(package private) void |
setModelClickability()
|
(package private) void |
setShapeState(java.util.Hashtable temp,
java.util.Hashtable temp2)
|
(package private) void |
setTranslucent(boolean isTranslucent,
java.util.BitSet bsSelected,
float translucentLevel)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
modelIndex
int modelIndex
modelVisibilityFlags
int modelVisibilityFlags
shape
BioShapeCollection shape
bioPolymer
BioPolymer bioPolymer
meshes
Mesh[] meshes
meshReady
boolean[] meshReady
mads
short[] mads
colixes
short[] colixes
paletteIDs
byte[] paletteIDs
bsColixSet
java.util.BitSet bsColixSet
bsSizeSet
java.util.BitSet bsSizeSet
bsSizeDefault
java.util.BitSet bsSizeDefault
isActive
boolean isActive
monomerCount
int monomerCount
monomers
Monomer[] monomers
wingVectors
javax.vecmath.Vector3f[] wingVectors
leadAtomIndices
int[] leadAtomIndices
hasBfactorRange
boolean hasBfactorRange
bfactorMin
int bfactorMin
bfactorMax
int bfactorMax
range
int range
floatRange
float floatRange
eightPiSquared100
private static final double eightPiSquared100
- See Also:
- Constant Field Values
BioShape
BioShape(BioShapeCollection shape,
int modelIndex,
BioPolymer bioPolymer)
calcBfactorRange
void calcBfactorRange()
calcMeanPositionalDisplacement
short calcMeanPositionalDisplacement(int bFactor100)
- Calculates the mean positional displacement in milliAngstroms.
http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html
> -----Original Message-----
> From: pdb-l-admin@sdsc.edu [mailto:pdb-l-admin@sdsc.edu] On
> Behalf Of Philipp Heuser
> Sent: Thursday, March 27, 2003 6:05 AM
> To: pdb-l@sdsc.edu
> Subject: pdb-l: temperature factor; occupancy
>
>
> Hi all!
>
> Does anyone know where to find proper definitions for the
> temperature factors
> and the values for occupancy?
>
> Alright I do know, that the atoms with high temperature
> factors are more
> disordered than others, but what does a temperature factor of
> a specific
> value mean exactly.
>
>
> Thanks in advance!
>
> Philipp
>
pdb-l: temperature factor; occupancy
Bernhard Rupp br@llnl.gov
Thu, 27 Mar 2003 08:01:29 -0800
* Previous message: pdb-l: temperature factor; occupancy
* Next message: pdb-l: Structural alignment?
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Isotropic B is defined as 8*pi**2.
Meaning: eight pi squared =79
so B=79*mean square displacement (from rest position) of the atom.
as u is in Angstrom, B must be in Angstrom squared.
example: B=79A**2
thus, u=sqrt([79/79]) = 1 A mean positional displacement for atom.
See also
http://www-structure.llnl.gov/Xray/comp/comp_scat_fac.htm#Atomic
for more examples.
BR
- Parameters:
bFactor100
-
- Returns:
- ?
findNearestAtomIndex
void findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
java.util.BitSet bsNot)
setMad
void setMad(short mad,
java.util.BitSet bsSelected,
float[] values)
setMad
private short setMad(int groupIndex,
short mad)
falsifyMesh
void falsifyMesh(int index,
boolean andNearby)
setColix
void setColix(short colix,
byte pid,
java.util.BitSet bsSelected)
setTranslucent
void setTranslucent(boolean isTranslucent,
java.util.BitSet bsSelected,
float translucentLevel)
setShapeState
void setShapeState(java.util.Hashtable temp,
java.util.Hashtable temp2)
setModelClickability
void setModelClickability()