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eyes:logics:normalmodeanalysis [2017/06/12 14:03]
bgraf
eyes:logics:normalmodeanalysis [2017/06/12 18:32] (current)
jschlie1
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-====== ​Normal Mode Analysis ​====== +====== ​NormalModeAnalysis ​====== 
-This logic performs a [[https://​i12r-studfilesrv.informatik.tu-muenchen.de/​wiki/​images/​1/​17/​Tirion1996_PRL.pdf| Normal Mode Analysis]] of the given 3d structure. It can be used to visualize basic molecular movement modes. ​+This logic performs a [[https://​i12r-studfilesrv.informatik.tu-muenchen.de/​wiki/​images/​1/​17/​Tirion1996_PRL.pdf| Normal Mode Analysis ]] (NMA) of the given 3D structure. It can be used to visualize basic molecular movement modes. ​
  
 ===== Usage ===== ===== Usage =====
-The logic has three modes that represent the three different major parts of NMA. In the first step the volume is filled with pseudo atoms. In the second step an elastic network is created with respect to the positions of the pseudo atoms. It is based on a Hessian Matrix and a cutoff distance. Last, eigenvector/​eigenvalue decomposition is performed and in a last step they are applied on the pseudoatoms. The workflow is split into 3 separate parts to allow the user to check intermediate results. ​+The logic has three modes that represent the three different major parts of NMA. In the first step the volume is filled with pseudo atoms. In the second step an elastic network is created with respect to the positions of the pseudo atoms. It is based on a Hessian Matrix and a cutoff distance. Last, eigenvector/​eigenvalue decomposition is performed and in a last step they are applied on the pseudoatoms. The workflow is split into 3 separate parts to allow the user to check intermediate results. A further discussion of NMA can be found [[https://​pdfs.semanticscholar.org/​9c62/​79a0ba18cfd94f893873a5c45271af9115bc.pdf|here]].
  
 ===== Modes ===== ===== Modes =====
-Choose between the three different NMA-steps //Fit Pseudo Atoms Into Volume//, //Compute Normal Modes// or //Apply Normal Modes//​. ​ 
- 
 ==== Fit Pseudo Atoms Into Volume ==== ==== Fit Pseudo Atoms Into Volume ====
-Fills the 3D volume with pseudo atoms. Two modes are accessible. Either //​Sphere ​Packing// that is filling out the whole volume or //Random// placing pseudo atoms in a randomized manner into the model volume. The lower the number of pseudo atoms of the NMA-model, the less the computational ​expensiveness ​for further applications+Fills the 3D volume with pseudo atoms. Two modes are accessible. Either //​Sphere ​packing// that is approximating ​the volume ​by densely packed spheres ​or //Random// placing pseudo atoms in a randomized manner into the model volume. The lower the number of pseudoatoms ​of the NMA-model, the less the computational ​costs for the following //Compute Normal Modes// application.
  
-  * **Pseudoatom Radius**: Radius of pseudoatoms in pixel. Should be 1.0 or more.  +|< 100% 30% >| 
-  * **Relative Pseudoatom Overlaps**: Determines how much of a given volume must be covered by a pseudoatom. Fully covered == 1.0. Note that a value between [0,1] means that pseudoatoms can intersect.+^ Parameters ​                ^ Description ​    ^ 
 +| Fitting mode  | Select whether the pseudoatoms shall be fitted into the density spherically or randomly. ​ | 
 +| -> Iterations | In case, "​Random"​ is selected as fitting mode, the number of iterations needs to be specified. | 
 +Pseudoatom Radius ​Radius of pseudoatoms in pixel. Should be 1.0 or more. | 
 +Relative Pseudoatom Overlaps ​Determines how much of a given volume must be covered by a pseudoatom. Fully covered == 1.0. Note that a value between [0,1] means that pseudoatoms can intersect. ​|
  
-**NOTE:​** ​ you can check the fitting result by double clicking the //​PseudoAtomVisualization// ​IO. You can also check the number of pseudoatoms by clicking on the 3d once.+**NOTE:​** ​ you can check the fitting result by double clicking the //​PseudoAtomVisualization// ​I/O. You can also check the number of pseudoatoms by clicking on the 3D once. 
 + 
 +|< 100% 30% >| 
 +^ Input                 ^ Description ​    ^ 
 +| Input 3D | 3D structure that is desired to be animated by NMA. | 
 + 
 +|< 100% 30% >| 
 +^ Output ​                ^ Description ​    ^ 
 +| Pseudoatom visualization | This is a test output to allow the user to check the result of the fitting process. The number of pseudoatoms can be shown by double clicking the IO and clicking the 3D structure afterwards. | 
 +| Pseudoatoms | Input file volume represented by pseudoatoms. |
  
 ==== Compute Normal Modes ==== ==== Compute Normal Modes ====
 Computes the normal modes for the  model consisting of pseudo atoms. ​ Computes the normal modes for the  model consisting of pseudo atoms. ​
  
-  * **Radius of interacting pseudoatoms**: The distance in pixel in which pseudoatoms affect each other.  +|< 100% 30% >| 
-  * **Lowest normal mode**: Lowest eigenvector to be calculated. Covers movement of more rigid areas.  +^ Parameters ​                ^ Description ​    ^ 
-  * **Highest normal mode**: Highest eigenvector to be calculated. Covers movements of more flexible domains and areas.  +Radius of interacting pseudoatoms ​The distance in pixel in which pseudoatoms affect each other. ​| 
-  * **Number of threads**: Number of threads to be used for data processing. Usually one per thread per CPU-core except for systems with Hyper-Threading.+Lowest normal mode Lowest eigenvector to be calculated. Covers movement of more rigid areas. ​| 
 +Highest normal mode Highest eigenvector to be calculated. Covers movements of more flexible domains and areas. ​| 
 +Number of threads ​Number of threads to be used for data processing. Usually one per thread per CPU-core except for systems with Hyper-Threading. ​|
  
-==== Apply Normal Modes ==== +|< 100% 30% >| 
-Applies ​the calculated normal modes and allows a selection between different states+^ Input                 ^ Description ​    ^ 
 +| Pseudoatoms | Model consisting of pseudoatoms from the //Fit Pseudo Atoms Into Volume//​-logic output|
  
-  * **(Normal Mode ; Amplitude) pairs**: Mode(s) to be displayed (== eigenvector(s) to be applied)To apply different modes at the same time you can use the following Syntax: (a;​b)(c;​d)(e;​f) while a,c,e are the modes (∈ N) and b,d,f the corresponding amplitudes (∈ R). The amount of applicable modes is limited by //Lowest Normal Mode/////​Highest Normal Mode// from the previous //Compute Normal Modes//​-logic+|< 100% 30% >| 
-  * **Number Of Intermediate States**: Determines how many single steps the final animation has. Equals to the final number ​of written 3Ds.  +^ Output ​                ^ Description ​    ^ 
- +| Collectivity Score | Visualization of score vsmode. The Collectivity Score is metric that describes ​the amount of collective motion of pseudo atoms within one mode. It is normalized between 0 and 1| 
-===== Inputs ===== +| Eigenvalues | Output ​of computed Eigenvalues| 
- +| Eigenvectors | Output ​of computed Eigenvectors|
-==== Fit Pseudo Atoms Into Volume ==== +
-**Input 3D**: 3D structure that is desired to be animated by NMA.  +
- +
-==== Compute Normal Modes ==== +
-**Pseudoatoms**:​ Model consisting ​of pseudoatoms from the //Fit Pseudo Atoms Into Volume//​-logic output.+
  
 ==== Apply Normal Modes ==== ==== Apply Normal Modes ====
-**Eigenvalues**:​ Eigenvalues resulting from the //Compute Normal Modes//​-logic output. +Applies ​the calculated normal modes and allows ​selection ​between ​different states
- +
-**Eigenvectors**:​ Eigenvectors resulting from the //Compute Normal Modes//​-logic output. +
- +
-**Pseudoatoms**:​ Model consisting of pseudoatoms from the //Fit Pseudo Atoms Into Volume//​-logic output. +
- +
-===== Outputs ===== +
- +
-==== Fit Pseudo Atoms Into Volume ==== +
-**Pseudoatom visualization**:​ This is a test output to allow the user to check the result of the fitting process. The number of pseudoatoms can be shown by double clicking the IO and clicking the 3D structure afterwards. +
- +
-**Pseudoatoms**:​ Input file volume represented by pseudoatoms.  +
- +
- +
-==== Compute Normal Modes ==== +
-**Collectivity Score**: Visualization of score vs. mode. The Collectivity Score is metric that describes the amount of collective motion of pseudo atoms within one mode. It is normalized ​between ​0 and 1.  +
- +
-**Eigenvalues**:​ Output of computed Eigenvalues. +
-  +
-**Eigenvectors**:​ Output of computed Eigenvectors.+
  
 +|< 100% 30% >|
 +^ Parameters ​                ^ Description ​    ^
 +| (Normal Mode ; Amplitude) pairs | Mode(s) to be displayed (== eigenvector(s) to be applied). To apply different modes at the same time you can use the following Syntax: (a;​b)(c;​d)(e;​f) while a,c,e are the modes (∈ N) and b,d,f the corresponding amplitudes (∈ R). The amount of applicable modes is limited by //Lowest Normal Mode/////​Highest Normal Mode// from the previous //Compute Normal Modes//​-logic. |
 +| Number Of Intermediate States | Determines how many single steps the final animation has. Equals to the final number of written 3Ds. |
  
 +|< 100% 30% >|
 +^ Input                 ^ Description ​    ^
 +| Eigenvalues | Eigenvalues resulting from the //Compute Normal Modes//​-logic output. |
 +| Eigenvectors | Eigenvectors resulting from the //Compute Normal Modes//​-logic output. |
 +| Pseudoatoms | Model consisting of pseudoatoms from the //Fit Pseudo Atoms Into Volume//​-logic output. |
  
 +|< 100% 30% >|
 +^ Output ​                ^ Description ​    ^
 +| Intermediate states | Sequence of 3Ds that represent the position of the molecule at discrete time steps. |