org.jmol.shapebio
class BioShape extends Object
Field Summary | |
---|---|
int | bfactorMax |
int | bfactorMin |
BioPolymer | bioPolymer |
BitSet | bsColixSet |
BitSet | bsSizeDefault |
BitSet | bsSizeSet |
short[] | colixes |
static double | eightPiSquared100 |
float | floatRange |
boolean | hasBfactorRange |
boolean | isActive |
int[] | leadAtomIndices |
short[] | mads |
Mesh[] | meshes |
boolean[] | meshReady |
int | modelIndex |
int | modelVisibilityFlags |
int | monomerCount |
Monomer[] | monomers |
byte[] | paletteIDs |
int | range |
BioShapeCollection | shape |
Vector3f[] | wingVectors |
Constructor Summary | |
---|---|
BioShape(BioShapeCollection shape, int modelIndex, BioPolymer bioPolymer) |
Method Summary | |
---|---|
void | calcBfactorRange() |
short | calcMeanPositionalDisplacement(int bFactor100)
Calculates the mean positional displacement in milliAngstroms.
|
void | falsifyMesh(int index, boolean andNearby) |
void | findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest) |
void | setColix(short colix, byte pid, BitSet bsSelected) |
void | setMad(short mad, BitSet bsSelected) |
short | setMad(int groupIndex, short mad) |
void | setModelClickability() |
void | setShapeState(Hashtable temp, Hashtable temp2) |
void | setTranslucent(boolean isTranslucent, BitSet bsSelected, float translucentLevel) |
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
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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: ?