It is normal, we hide them on purpose.
MyAtom class inherits from SBAtom, yes. I will try to produce a very small example so I can paste the entire file.
Edit: This is a small full sample
<SAMSON>
<majorVersionNumber> 0 </majorVersionNumber>
<minorVersionNumber> 7 </minorVersionNumber>
<patchVersionNumber> 0 </patchVersionNumber>
<numberOfNodeTypes> 13 </numberOfNodeTypes>
<nodeTypes>
<nodeType>
<nodeTypeIndex> 0 </nodeTypeIndex>
<className> MySidechain </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 1 </nodeTypeIndex>
<className> MyBackbone </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 2 </nodeTypeIndex>
<className> MyChain </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 3 </nodeTypeIndex>
<className> MyStructuralModel </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 4 </nodeTypeIndex>
<className> MyStructuralGroup </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 5 </nodeTypeIndex>
<className> MyResidue </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 6 </nodeTypeIndex>
<className> MyAtom </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 7 </nodeTypeIndex>
<className> MyStructuralGroup2 </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 8 </nodeTypeIndex>
<className> MyStructuralGroup3 </className>
<elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 1.0.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 9 </nodeTypeIndex>
<className> SBMStructuralModelNodeRoot </className>
<elementUUID> 5A3CE002-9368-1EAF-7DBA-66567958AB1F </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 0.7.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 10 </nodeTypeIndex>
<className> SBDDocumentCamera </className>
<elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 0.7.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 11 </nodeTypeIndex>
<className> SBDDocumentLayer </className>
<elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 0.7.0 </classVersionNumber>
</nodeType>
<nodeType>
<nodeTypeIndex> 12 </nodeTypeIndex>
<className> SBDDocument </className>
<elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID>
<sdkVersionNumber> 0.7.0 </sdkVersionNumber>
<classVersionNumber> 0.7.0 </classVersionNumber>
</nodeType>
</nodeTypes>
<numberOfNodes> 21 </numberOfNodes>
<nodes>
<nodeTypeIndex> 12 </nodeTypeIndex>
<nodeTypeIndex> 10 </nodeTypeIndex>
<nodeTypeIndex> 11 </nodeTypeIndex>
<nodeTypeIndex> 3 </nodeTypeIndex>
<nodeTypeIndex> 9 </nodeTypeIndex>
<nodeTypeIndex> 7 </nodeTypeIndex>
<nodeTypeIndex> 4 </nodeTypeIndex>
<nodeTypeIndex> 8 </nodeTypeIndex>
<nodeTypeIndex> 6 </nodeTypeIndex>
<nodeTypeIndex> 2 </nodeTypeIndex>
<nodeTypeIndex> 5 </nodeTypeIndex>
<nodeTypeIndex> 1 </nodeTypeIndex>
<nodeTypeIndex> 6 </nodeTypeIndex>
<nodeTypeIndex> 0 </nodeTypeIndex>
<nodeTypeIndex> 6 </nodeTypeIndex>
<nodeTypeIndex> 2 </nodeTypeIndex>
<nodeTypeIndex> 5 </nodeTypeIndex>
<nodeTypeIndex> 1 </nodeTypeIndex>
<nodeTypeIndex> 6 </nodeTypeIndex>
<nodeTypeIndex> 0 </nodeTypeIndex>
<nodeTypeIndex> 6 </nodeTypeIndex>
</nodes>
<nodeContents>
<node>
<index> 0 </index>
<expandedFlag> 1 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<numberOfCameras> 1 </numberOfCameras>
<nodeIndex> 1 </nodeIndex>
<numberOfLayers> 1 </numberOfLayers>
<nodeIndex> 2 </nodeIndex>
<numberOfGroups> 0 </numberOfGroups>
<numberOfStoredConformations> 0 </numberOfStoredConformations>
<numberOfStoredPaths> 0 </numberOfStoredPaths>
<activeCameraIndex> 1 </activeCameraIndex>
<activeLayerIndex> 2 </activeLayerIndex>
</node>
<node>
<index> 1 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<name> Camera 1 </name>
<eyePosition>
<v[0]> 0 </v[0]>
<v[1]> 0 </v[1]>
<v[2]> 10000 </v[2]>
</eyePosition>
<targetPosition>
<v[0]> 0 </v[0]>
<v[1]> 0 </v[1]>
<v[2]> 0 </v[2]>
</targetPosition>
<upVector>
<v[0]> 0 </v[0]>
<v[1]> 1 </v[1]>
<v[2]> 0 </v[2]>
</upVector>
<nearPlane> 100 </nearPlane>
<farPlane> 2e+06 </farPlane>
<aspectRatio> 1.41675 </aspectRatio>
<fieldOfViewAngleY> 19 </fieldOfViewAngleY>
<inertiaFlag> 0 </inertiaFlag>
</node>
<node>
<index> 2 </index>
<expandedFlag> 1 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<name> Layer 1 </name>
<numberOfModels> 1 </numberOfModels>
<nodeIndex> 3 </nodeIndex>
<numberOfSimulators> 0 </numberOfSimulators>
<numberOfControllers> 0 </numberOfControllers>
<numberOfLabels> 0 </numberOfLabels>
<hasActiveModel> 0 </hasActiveModel>
</node>
<node>
<index> 3 </index>
<expandedFlag> 1 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<name> Structural model </name>
<rootIndex> 4 </rootIndex>
<propertyFlags> 0 </propertyFlags>
<backboneNeighborGridInitialized> 0 </backboneNeighborGridInitialized>
</node>
<node>
<index> 4 </index>
<expandedFlag> 1 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> Nodes </name>
<numberOfChildren> 3 </numberOfChildren>
<nodeIndex> 5 </nodeIndex>
<nodeIndex> 9 </nodeIndex>
<nodeIndex> 15 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 5 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> Double Strand 1 </name>
<numberOfChildren> 1 </numberOfChildren>
<nodeIndex> 6 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 6 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> Base Segment 4099 </name>
<numberOfChildren> 2 </numberOfChildren>
<nodeIndex> 7 </nodeIndex>
<nodeIndex> 8 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 7 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> Base Pair 4100 </name>
<numberOfChildren> 0 </numberOfChildren>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 8 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 0 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<position>
<v[0]> -877.886 </v[0]>
<v[1]> 516.92 </v[1]>
<v[2]> 0.0153761 </v[2]>
</position>
<element> 109 </element>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 9 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> Single Strand 1 </name>
<numberOfChildren> 1 </numberOfChildren>
<nodeIndex> 10 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 10 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> N4102 </name>
<numberOfChildren> 2 </numberOfChildren>
<nodeIndex> 11 </nodeIndex>
<nodeIndex> 13 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
<residueType> 36 </residueType>
<residueTypeString> </residueTypeString>
</node>
<node>
<index> 11 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> N4102 Backbone </name>
<numberOfChildren> 1 </numberOfChildren>
<nodeIndex> 12 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 12 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 0 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<position>
<v[0]> -970.453 </v[0]>
<v[1]> -85.8914 </v[1]>
<v[2]> 538.434 </v[2]>
</position>
<element> 99 </element>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 13 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> N4102 Sidechain </name>
<numberOfChildren> 1 </numberOfChildren>
<nodeIndex> 14 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 14 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 0 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<position>
<v[0]> -880.731 </v[0]>
<v[1]> 352.262 </v[1]>
<v[2]> 220.392 </v[2]>
</position>
<element> 100 </element>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 15 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> Single Strand 2 </name>
<numberOfChildren> 1 </numberOfChildren>
<nodeIndex> 16 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 16 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> N4108 </name>
<numberOfChildren> 2 </numberOfChildren>
<nodeIndex> 17 </nodeIndex>
<nodeIndex> 19 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
<residueType> 36 </residueType>
<residueTypeString> </residueTypeString>
</node>
<node>
<index> 17 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> N4108 Backbone </name>
<numberOfChildren> 1 </numberOfChildren>
<nodeIndex> 18 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 18 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 0 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<position>
<v[0]> -788.488 </v[0]>
<v[1]> 1018.95 </v[1]>
<v[2]> -570.406 </v[2]>
</position>
<element> 99 </element>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 19 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 1 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<name> N4108 Sidechain </name>
<numberOfChildren> 1 </numberOfChildren>
<nodeIndex> 20 </nodeIndex>
<propertyFlags> 0 </propertyFlags>
</node>
<node>
<index> 20 </index>
<expandedFlag> 0 </expandedFlag>
<visibilityFlag> 0 </visibilityFlag>
<hasMaterial> 0 </hasMaterial>
<mobilityFlag> 1 </mobilityFlag>
<position>
<v[0]> -874.781 </v[0]>
<v[1]> 804.363 </v[1]>
<v[2]> -159.697 </v[2]>
</position>
<element> 100 </element>
<propertyFlags> 0 </propertyFlags>
</node>
</nodeContents>
</SAMSON>
The atoms below the Sidechain and Backbone are not created when reading the same, but the atom below the structural group is.
Thanks!