Package org.jmol.shapebio

Class BioShape

    • Field Detail

      • modelIndex

        public int modelIndex

      • modelVisibilityFlags

        public int modelVisibilityFlags

      • meshes

        public Mesh[] meshes

      • meshReady

        public boolean[] meshReady

      • colixesBack

        public short[] colixesBack

      • monomers

        public Monomer[] monomers

      • wingVectors

        public javajs.util.V3[] wingVectors

      • leadAtomIndices

        int[] leadAtomIndices

      • hasBfactorRange

        boolean hasBfactorRange

      • bfactorMin

        int bfactorMin

      • bfactorMax

        int bfactorMax

      • range

        int range

      • floatRange

        float floatRange

    • Method Detail

      • setProperty

        public void setProperty​(java.lang.String propertyName,
                        java.lang.Object value,
                        BS bsSelected)
        Specified by:
        setProperty in class Shape

      • 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

        public void findNearestAtomIndex​(int xMouse,
                                 int yMouse,
                                 Atom[] closest,
                                 BS bsNot)
        Overrides:
        findNearestAtomIndex in class Shape

      • setMad

        void setMad​(short mad,
            BS bsSelected,
            float[] values)

      • getMad

        private short getMad​(int groupIndex,
                     short mad)

      • falsifyMesh

        public void falsifyMesh()

      • falsifyNearbyMesh

        private void falsifyNearbyMesh​(int index)

      • setColixBS

        void setColixBS​(short colix,
                byte pid,
                BS bsSelected)

      • setColixBack

        void setColixBack​(short colix,
                  BS bsSelected)

      • setColixes

        void setColixes​(short[] atomColixes,
                BS bsSelected)

      • setParams

        public void setParams​(java.lang.Object[] data,
                      int[] atomMap,
                      BS bsSelected)

      • setTranslucent

        void setTranslucent​(boolean isTranslucent,
                    BS bsSelected,
                    float translucentLevel)

      • getBioShapeState

        void getBioShapeState​(java.lang.String type,
                      boolean translucentAllowed,
                      java.util.Map<java.lang.String,​BS> temp,
                      java.util.Map<java.lang.String,​BS> temp2)