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​(String propertyName,
                                Object value,
                                javajs.util.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
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         Isotropic B is defined as 8*pi**2<u**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,
                                         javajs.util.BS bsNot)
        Overrides:
        findNearestAtomIndex in class Shape
      • setMad

        void setMad​(short mad,
                    javajs.util.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,
                        javajs.util.BS bsSelected)
      • setColixBack

        void setColixBack​(short colix,
                          javajs.util.BS bsSelected)
      • setColixes

        void setColixes​(short[] atomColixes,
                        javajs.util.BS bsSelected)
      • setParams

        public void setParams​(Object[] data,
                              int[] atomMap,
                              javajs.util.BS bsSelected)
      • setTranslucent

        void setTranslucent​(boolean isTranslucent,
                            javajs.util.BS bsSelected,
                            float translucentLevel)
      • getBioShapeState

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