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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

• All atoms with the name chosen by the user with the range of residues given will be used to as the template basis of the overlap.

• All atoms in molecule 2 will be transformed during the overlap onto molecule 1.

• Generally, satisfactory overlap is achieved and a stable inverse is found using 5 to 20 atoms. If your structure is more dynamic and you are using this tool for further quantitative analysis then a larger number of basis atoms may be used.

• The two molecules do not need to be of the same type for the algorithm to work. The files and basis templates only need to have the same number of points. At least three atomic positions are required.

• Only one structure is required in the trajectory file. This allows one to overlap coordinates in one molecule in one PDB file onto the coordinates of another.

• Even if only one structure is to be overlapped, it still needs a reference structure.

• The default output file format is DCD. If you wish to save the aligned coordinates as a PDB file then type in a filename with .pdb at the end. For large numbers of frames we recommend saving your data in the DCD format (~seven fold smaller file size).

• Optional inputs are provided to handle complex structures to specifiy the atoms to be used as the basis template where it could be redundant. See the Advanced Usage section below.

• An Advanced Input checkbox is provided to specify whether to use a Z coordinate filter to ignore all frames that contain ANY atoms with a Z value less the cutoff value. See the Advanced Usage section below.

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.

• run name: user defined name of folder that will contain the results.

Molecule 1 [reference structure]

• reference structure (mol 1): PDB file with coordinates that molecule 2 will be overlapped onto.
• alignment basis (mol 1): Atom name to be used for the overlap.
• low residue (mol 1): Residue number where the overlap will begin.
• high residue (mol 1): Residue number where the overlap will end.

Molecule 2 [structure(s) to align]

• reference structure (mol 2): PDB file with naming information for coordinates that will be overlapped onto molecule 1.
• coordinates to be aligned: pdb or dcd: PDB or DCD file with coordinates that will be overlapped onto molecule 1.
• output filename (aligned mol 2): Name of output PDB or DCD file with the aligned coordinates.
• alignment basis (mol 2): Atom name to be used for the overlap.
• low residue (mol 2): Residue number where the overlap will begin.
• high residue (mol 2): Residue number where the overlap will end.

Example Output

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).

Files Used and Created in Example

• input files

  hiv1_gag.pdb
  hiv1_gag_200_frames.dcd

• output files

  aligned_hiv1_gag_200_frames.dcd
  aligned_hiv1_gag_200_frames.dcd.minmax

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.

• extra basis description (mol 1): Input a string to refine the selection basis described in the general input section for molecule 1. Default = None.

• extra basis description (mol 2): Input a string to refine the selection basis described in the general input section for molecule 2. Default = None.

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.

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

Example Output (Optional Input)

-><-

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).

Files Used and Created in Example (Optional Input)

• input files

  mab.pdb
  mab_100_frames.dcd

• output files

  aligned_mab_100_frames.dcd
  aligned_mab_100_frames.dcd.minmax

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.

• Check Box for Advanced Input: check to reveal the Advanced Input options.

• check box to use Z coordinate filter: check to activate the Z coordinate filter

• Z cutoff (Angstroms): The Z cutoff value in Angstroms

Example Output (Advanced Input)

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)

• input files

  hiv1_gag.pdb
  hiv1_gag_200_frames.dcd

• output files

  aligned_hiv1_gag_zcutoff.dcd
  aligned_hiv1_gag_zcutoff.dcd.minmax

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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