3.4 Managing Models
This feature is only available for entries with more than one model in the pdb file!
Sometimes you can find a pdb file that contains multiple models. A model describes a conformation of a molecule at a specific timestamp. Therefore, each model contains the same atoms, in a different alignment.
The MembraneEditor only regards atoms of one particular timestamp per entry. Otherwise, it would have to generate many timestemps in the finished membrane, needing a huge amount of disc space and making further use of the membrane impossible to use any further.
This requires you to define the model that should be used when adding a multi model instance.
By default, the first model will be activated when importing a new file. It can be changed by using the 'Change Model' button in the context menu.
The file will then be opened in the 3D environment of the Membrane View.
The Molecular View in model change mode
You will notice that the lower toolbar looks different now. For instance, you will see the following field now:
The number in the box shows the number of the currently selected model. Use this box in order to select another model. Afterwards, you can see that the conformation of the molecule has changed.
When finished, press the 'Apply' button on the left in order to activate the new model for the entry. Otherwise, the change will be discarded.
Note that if you change a model via the Database View, the changes will only affect new instances in the membrane. The model of those already in use (including in other membranes) will remain.
You can, however, also change the current model of individual molecules
that have already been added to the membrane by rightclicking on them.
- Written by bjoern
- Category: Cm2help 3. Managing local PDB Files
- Published: 14 September 2013
- Hits: 2071