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Extract Utilities

Allows user to extract individual structures and/or SAS profiles from a larger input structure file and/or folder containing SAS profiles.

Accessibility

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

Basic Usage

The purpose of the module is create new files with coordinates extracted from larger files and/or a new folder with a subset of SAS profiles. There are six possible modes of use. In the following the "/" separator is used to indicate "either or both".

  1. Extract a structure / SAS profile from a single frame / profile
  2. Extract structures / SAS profiles from range of frames / profiles
  3. Extract any number of structures / SAS profiles with frames / profiles listed in a user supplied "text" file
  4. Extract any number of structures / SAS profiles with frames / profiles listed in a user supplied "weights" file
  5. Extract structures / SAS profiles at a user supplied sampling frequency
  6. Extract all structures / SAS profiles (useful to convert structure file type)

An example of each use case is shown below.

Notes

Screen Shots and Description of Input Fields

This example extracts structures and SAS profiles using each of the use cases mentioned above, assuming that the SAS profiles were calculated using SasCalc. If a different SAS module was used to calculate the SAS profiles, the SAS type and SAS data path must be selected accordingly. Usage where only structures or only SAS profiles are extracted are not shown, but the input fields for the individual cases does not change in these conditions.

Case 1: Single Frame

This example extracts a structure from frame 7 and its corresponding SAS profile. Note that the sascalc/neutron_D2Op_100 directory is selected to extract SAS profiles only for that particular contrast.

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Case 2: Range

This example extracts frames 3 through 22 inclusive.

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Case 3: Text File

The sample input text file contains a list of six frames to extract. This file must have at least one line. The final frame number must not exceed the number of rames in the input PDB/DCD file.

6
7
8
9
10
88

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Case 4: Weights File

The sample input weights file contains a list of frames to extract. In the box below only the first few lines are shown. The number of lines in this file must match the number of rames in the input PDB/DCD file.


# file generated on Sun Apr 12 18:05:32 2015
# structure, X2, weight  
1   10.394808   0.000000
2   8.041527    0.000000
3   8.792317    0.000000
4   8.217490    0.000000
5   6.896897    1.000000
6   7.555859    1.000000
7   8.220753    0.000000
. . .

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Case 5: Periodic

The sample input directs the program to save every tenth structure and it's associated SAS profile.

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Case 6: All

The example is shown to convert an input PDB file to DCD. One can also use this option to convert an input DCD to PDB by reading in a DCD trajectory file and indicating a file name with the suffix ".dcd". Note that longer trajectories should be maintained in DCD files.

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Case 7: Single Frame: Multiple Contrasts (sascalc SAS type only)

The example is shown to extract frame 7 from a dcd file and its corresonding SAS profiles from multiple directories (from SasCalc calculations at different contrasts). Note the difference in SAS data path from Case 1 above. The top level /sascalc directory is selected rather than the contrast-specific directory, /sascalc/neutron_D2Op_100.

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Example Output

Results will be written to a new directory within the given "run name". For example, in the figure it is noted that the structures were saved files within the current project directory within the chosen "run name" directory. SAS profile(s) are saved to a new directory named by the input SAS profile type as shown below:

Case 1: Single Frame

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./run_0/extract_utilities/hiv1_gag_frame_7.pdb
./run_0/extract_utilities/sascalc/neutron_D2Op_100

Case 2: Range

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./run_0/extract_utilities/hiv1_gag_frames_3_22.dcd
./run_0/extract_utilities/sascalc/neutron_D2Op_100

Case 3: Text File

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./run_0/extract_utilities/hiv1_gag_frames_text_file.dcd
./run_0/extract_utilities/sascalc/neutron_D2Op_100

Case 4: Weights File

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./run_0/extract_utilities/hiv1_gag_frames_weights_file.dcd
./run_0/extract_utilities/sascalc/neutron_D2Op_100

Case 5: Periodic

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./run_0/extract_utilities/hiv1_gag_frames_periodic.dcd
./run_0/extract_utilities/sascalc/neutron_D2Op_100

Case 6: All

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./run_0/extract_utilities/hiv1_gag.dcd

Case 7: Single Frame: Multiple Contrasts (sascalc SAS type only)

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Note the difference between this output and that for Case 1 above. The SAS files corresponding to frame 7 are extracted from all directories below the top level /sascalc directory, i.e., /neutron_D2Op_100 and /neutron_D2Op_0.


./run_0/extract_utilities/hiv1_gag_frame_7.pdb
./run_0/extract_utilities/sascalc/neutron_D2Op_100
./run_0/extract_utilities/sascalc/neutron_D2Op_0

Visualization

None

Files Used and Created in Examples

NOTE: input and output SAS profiles are not available for download since they cannot be uploaded to test the module.

Limitations

Only PDB and DCD file formats are supported. SAS profiles must exist on the server as there is no option to upload a folder containg such files.

Reference(s) and Citations

Not published.

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