9.5 Rebuild Membrane Model from existing pdb file
Usually, the MembraneEditor can only read existing membranes out of .Cm2 files. There is, however, a special feature which allows you to parse existing membranes from their pdb-files. This can be useful if a membrane should be altered in the meantime with another application, like a molecular dynamics tool.
Rebuilding a membrane model is only possible if :
a) the membrane data is still available, either from a corresponding .Cm2 file or from the attached membrane model within the pdb file (if attaching has been enabled earlier)
b) only the positions of the atoms have been altered, not their counts
In order to start the attempt, use 'Rebuild Membrane Model' inside the file menu
Now you have to select the pdb-file of the membrane you want to rebuild. After doing so, the membrane will be restored, assuming that the membrane model has been attached into the file. Otherwise, or if the data has been deleted by another application, you will be prompted to select the corresponding .Cm2 file.
If no further information about coordinate transformations are found, you'll need to remember them (you defined them inside compatibility dialog). The following dialog will appear:
Enter the settings used while generating the original membrane in order to get a correct result and proceed afterwards.
You'll also get the option to repair the file after successful rebuilding and to produce a backup file of the original membrane you used.
The atom positions of the molecules are updated afterwards, but the shape represenations will not change their outer appearance. This means, that all lipids of one type share still the same shape. As a logical consequence, if you want to make further computations, you are adviced to use only atom collisions and to toggle of the shape collisions in the 3D Settings dialog.
- Written by bjoern
- Category: Cm2help 9. Generating Output
- Published: 14 September 2013
- Hits: 2042