Cast structure tool (alpha version)
A simple homology modelling tool
Toni Giorgino — © Universitat Pompeu Fabra 2010
The Cast structure tool is a modeling plugin for VMD. It copies the coordinates of a selection A another selection B, but preserves A's topology. Coordinates of A's atoms will be copied verbatim when an unambiguous match exists in B; otherwise, the new coordinates will be guessed with a local fit.
In other words, it performs a "smart coordinate copy" operation between molecules with different topologies, allowing you to make minor topological changes while preserving a protein's higher structure.
The main use of the tool is to introduce small topological changes in otherwise "good" structures. In fact you can:
- modify structures, e.g. adding/removing caps
- mutate residues (e.g. with AMBER topology)
- make "compatible" structures of proteins in different conformations from non-matching PDB files (simple homology modeling)
Usage
The plugin is accessible from VMD in Extensions > Modeling > Cast structure.
You will need two PDB files loaded:
- a system, likely one that you intend to simulate, of which you want to preserve the topology. The coordinates of its atoms, instead, you want to be taken from...
a topologically similar, but not quite identical, structure; topologically similar may mean e.g. different capping, subsetting, presence of mutated residues, and the like.
The Cast Structure Tool will perform a "smart" copy of coordinates of B into A, while preserving A's topology (i.e. atom number, order and types). Specifically, after the cast operation,
- the topology of A will be unchanged
- atoms in A which have an unambiguous counterpart in B will be moved in order to overlap them
- atoms in A not in B will be moved following the local residue or sequence
- atoms in B with no correspondence in A will be ignored
- atoms not matched by the atom selections are ignored
The "local fit" is computed considering the matched atoms inside the same residue (if there is at least N of them) or the matching atoms in the M surrounding residues (otherwise).
Note that the cast operation is purely based on geometry and does not keep into account the molecular forcefield. It is therefore highly recommended that you minimize the structures resulting from the cast operation.
Screenshot
Examples
Download the files required by these examples from the archive cast_structure_example.tgz.
Example 1: cast an all-atom topology onto known heavy-atom positions
Load the all-atom model kx.pdb (set as top molecule) and the heavy-atom model k.pdb (assume it is molecule id 1).
- Invoke the Cast Structure Tool GUI.
Specify all in both the selection boxes, then click Cast will perform the cast operation.
- Notice that Lys136 is poorly guessed, because its different side-chain shape somewhat conflicts with the positions of atoms "copied verbatim". Minimization will fix the problem.
- As an alternative, select the "fit" rather than "copy" option for exactly-matched
atoms. In this way, all of A's atoms will be fit, resulting in lesser distortion but also less faithful matches to B's atoms positions.
Example 2: cast an all-atom topology onto known CA's positions
Load the all-atom model kx.pdb (set as top molecule) and kca.pdb (assume it is molecule id 1).
As a first attempt, we will cast all of top onto all of molecule 1.
- Note that the outcome is an error, because chain A of top molecule (printed on console) does not have matches nor a "local environment".
The correct way is to cast chain B of top onto all of molecule 1.
Installation
Download the plugin source and follow the instructions therein.
Licensing
This is alpha software. By downloading the software you agree to comply with the terms of GPL version 2. The Tool may be described in a forthcoming publication. You are kindly requested check here if a citation is available when publishing results obtained with the tool.
Acknowledgments
Work partially supported by the VPH-NoE.
