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Align

Transforms structure(s) from an input structure file so that they overlap with a reference input structure.


Accessibility

The Align module is accessible from the Tools section of the main menu.


Basic Usage

The purpose of the module is to align a single structure or an entire trajectory onto a reference structure.

Users will input a reference PDB file name and choose an atom name and range of residues as the basis template for the overlap. Additionally, users will input a reference PDB file name, the file name of a trajectory file (in either PDB or DCD format) along with an atom name and range of residues as the basis template for the overlap.


Notes


Screen Shots and Description of Input Fields


This example overlaps a trajectory of 200 structures onto a reference structure using CA atoms within residue numbers 145 to 350.


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Molecule 1 [reference structure]



Molecule 2 [structure(s) to align]



Example Output

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The output will indicate the number of frames, the minimum, maximum and total range of dimensions for the structures in the aligned file.

Results will be written to a new directory within the given "run name". For example, in the figure it is noted that the structures and dimensions were saved files within the current project directory within the chosen "run name" directory:


./run_0/align/aligned_hiv1_gag_200_frames.dcd  

./run_0/align/aligned_hiv1_gag_200_frames.dcd.minmax

Visualization

An llustration of the alignment process. In the figure below, the molecule 1 (A), molecule 2 (B), and molecule 2 aligned onto molecule 1 (C) are shown. The alignment basis CA atoms are shown as blue (molecule 1) or red (molecule 2) balls. In all three panels, the first CA atom for resid 145 is shown as a yellow ball. Only one frame of molecule 2 is shown in panels (B) and (C).

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Files Used and Created in Example


Advanced Usage


Optional Input

In some cases you may have a molecule that has many chains and/or segments that have identical residue numbering and thus one may want to limit the overlap basis to a single chain or segment.

Note that the syntax for the input is specific. To select a segment named "SEG1" one would type

segname[i] == "SEG1"

the extra characters ( [i] and == ) are required, sine your input string is evaluated directly by the program. For example to select chain A on would type

chain[i] == "A"

Depending on your needs, the extra basis description is optional for both molecule 1 and molecule 2.


In the example below, a protein structure composed of several independent polymer chains (as depicted in the diagram below) are overlapped on one of the chains. Extra basis options are required in this case since each chain has the same residue range and atoms and thus the overlap basis is not uniquely defined.

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This example overlaps a trajectory of 100 structures onto a reference structure using CA atoms within residue numbers 10 to 20 in chain L.


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Example Output (Optional Input)

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Results will be written to a new directory within the given "run name". For example, in the figure it is noted that the structures and dimensions were saved files within the current project directory within the chosen "run name" directory:


./run_0/align/aligned_mab_100_frames.dcd  

./run_0/align/aligned_mab_100_frames.dcd.minmax

Visualization (Optional Input)

An llustration of the alignment process. In the figure below, the molecule 1 (A), molecule 2 (B), and molecule 2 aligned onto molecule 1 (C) are shown. The alignment basis CA atoms are shown as blue (molecule 1) or red (molecule 2) balls. In all three panels, the first CA atom for resid 10 is shown as a yellow ball. Only one frame of molecule 2 is shown in panels (B) and (C).

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Files Used and Created in Example (Optional Input)


Advanced Input

In some cases you may want to limit your trajectory file to structures that have Z coordinates above a threshold value so that you can model molecules on a surface, for example. This can be accomplished using the Advanced Input option at the bottom of the page.


This example overlaps a trajectory of 200 structures onto a reference structure using CA atoms within residue numbers 145 to 350, ignoring all frames in which ANY atom has a Z coordinate less than -66.0.


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Example Output (Advanced Input)

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The output will indicate the number of frames, the minimum, maximum and total range of dimensions for the structures in the aligned file. Note that only 122 of the original 200 frames were written due to the choice of Z cutoff.

Results will be written to a new directory within the given "run name". For example, in the figure it is noted that the structures and dimensions were saved files within the current project directory within the chosen "run name" directory:


./run_0/align/aligned_hiv1_gag_zcutoff.dcd  

./run_0/align/aligned_hiv1_gag_zcutoff.dcd.minmax

Files Used and Created in Example (Advanced Input)


Limitations

The program is written so that linear polymers are handled over a specific selection of residues.


Reference(s) and Citations

  1. A solution for the best rotation to relate two sets of vectors W. Kabsch, Acta Crystallog. sect. A 32 922-923 (1976). BIBTeX, EndNote, Plain Text

  2. A discussion of the solution for the best rotation to relate two sets of vectors W. Kabsch, Acta Crystallog. sect. A 34 827-828 (1978). BIBTeX, EndNote, Plain Text

  3. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger, Comp. Phys. Comm. 183, 382-389 (2012). BIBTeX, EndNote, Plain Text


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