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Build Utilities

Methods to modify PDB files and structures to help build starting structures for modeling.


Accessibility

The Build Utilities module is accessible from the Beta section of the main menu.


Basic Usage

The purpose of this module is to modify or create new PDB files to enable the generation of starting structures for simulation and analysis. There are two types of methods one can use:

* pdb utilities : to modify PDB files

* fasta utilities : to create a sequence PDB file from a fasta sequence (no coordinates)

There are several ways one can use pdb utilites to modify input pdb files. This includes renumbering indexes, renumbering residues, modifing pdb fields to generate internal flags in the file to indicate which atoms are to be held fixed in a simulation, general pdb field modfication based on user supplied selections, methods to translate & rotate coordinates and methods to align the molecule on principal axes. The output of any of the methods in pdb utilities is a new PDB file.

As stated above, the purpose of fasta utilities is to create a new PDB file that contains a single atom per residue from a user supplied fasta sequence for either proteins or nucleic acids. This type of "sequence" PDB file is useful to generate complete structures using programs like psfgen.

Examples of each option are shown in examples below.


Notes


Screen Shots and Description of Input Fields

The default input parameters for each use case are shown below in the particular examples. Both pdb utilities and fasta utilities require a run name input parameter

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PDB Utilities Options

PDB utilities requires an input pdb file and to select one of the modification options.

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Note that the translate/rotate & align on pmi modules will alter the coordinates in the original pdb file based on the

user selected operations. It possible to alter coordinates using modify pdb fields as shown below.

Case 1: PDB Utilities : Renumber Indices/Residues

The renumber indices/residues pdb utility option has several input fields.

One or both of the following checkboxes must be selected:

Indices and/or residue numbers will increment for each atom and/or residue in the entire file starting with the user

supplied value(s).

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Here is an example of renumbering an input pdb file where the indices are renumbered from 23 and residue numbers from 47.

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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 a new pdb file was saved in the current project directory within the chosen "run name" directory:


run_0/build_utilities/renumbered.pdb

Inspecting the first few lines of the original and final pdb files highlights the changes.


ATOM      1  N   GLY X   1     -21.525 -67.562  86.759  1.00  0.00      GAG  N 
ATOM      2  HT1 GLY X   1     -22.003 -68.460  86.892  1.00  0.00      GAG  H
ATOM      3  HT2 GLY X   1     -21.905 -66.929  87.525  1.00  0.00      GAG  H
ATOM      4  HT3 GLY X   1     -20.492 -67.726  86.876  1.00  0.00      GAG  H
ATOM      5  CA  GLY X   1     -21.725 -66.910  85.457  1.00  0.00      GAG  C
ATOM      6  HA1 GLY X   1     -21.476 -67.600  84.661  1.00  0.00      GAG  H
ATOM      7  HA2 GLY X   1     -21.157 -65.997  85.450  1.00  0.00      GAG  H
ATOM      8  C   GLY X   1     -23.103 -66.411  85.215  1.00  0.00      GAG  C
ATOM      9  O   GLY X   1     -23.249 -65.504  84.385  1.00  0.00      GAG  O
ATOM     10  N   ALA X   2     -24.180 -66.939  85.847  1.00  0.00      GAG  N
ATOM     11  HN  ALA X   2     -24.180 -67.788  86.402  1.00  0.00      GAG  H
ATOM     12  CA  ALA X   2     -25.441 -66.230  85.763  1.00  0.00      GAG  C

ATOM     23 N    GLY X  47     -21.525 -67.562  86.759  1.00  0.00      GAG  N  
ATOM     24 HT1  GLY X  47     -22.003 -68.460  86.892  1.00  0.00      GAG  H  
ATOM     25 HT2  GLY X  47     -21.905 -66.929  87.525  1.00  0.00      GAG  H  
ATOM     26 HT3  GLY X  47     -20.492 -67.726  86.876  1.00  0.00      GAG  H  
ATOM     27 CA   GLY X  47     -21.725 -66.910  85.457  1.00  0.00      GAG  C  
ATOM     28 HA1  GLY X  47     -21.476 -67.600  84.661  1.00  0.00      GAG  H  
ATOM     29 HA2  GLY X  47     -21.157 -65.997  85.450  1.00  0.00      GAG  H  
ATOM     30 C    GLY X  47     -23.103 -66.411  85.215  1.00  0.00      GAG  C  
ATOM     31 O    GLY X  47     -23.249 -65.504  84.385  1.00  0.00      GAG  O  
ATOM     32 N    ALA X  48     -24.180 -66.939  85.847  1.00  0.00      GAG  N  
ATOM     33 HN   ALA X  48     -24.180 -67.788  86.402  1.00  0.00      GAG  H  
ATOM     34 CA   ALA X  48     -25.441 -66.230  85.763  1.00  0.00      GAG  C  

Files Used and Created in Example


Case 2: PDB Utilities : Make Constraint File(s)

The make constraint file(s) pdb utility option has several input fields. Note that the method allows you to generate multiple constraint files in a single run. All atoms that satisify the selected option will have the value in the selected field changed to 1.00.

The default inputs are shown below.

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Here is an example of modifying an input pdb file where the beta field is set to 1.00 for heavy atoms (non-hydrogen).

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Inspecting the first few lines of the original and final pdb files highlights the changes.


ATOM      1  N   GLY X   1     -21.525 -67.562  86.759  1.00  0.00      GAG  N 
ATOM      2  HT1 GLY X   1     -22.003 -68.460  86.892  1.00  0.00      GAG  H
ATOM      3  HT2 GLY X   1     -21.905 -66.929  87.525  1.00  0.00      GAG  H
ATOM      4  HT3 GLY X   1     -20.492 -67.726  86.876  1.00  0.00      GAG  H
ATOM      5  CA  GLY X   1     -21.725 -66.910  85.457  1.00  0.00      GAG  C
ATOM      6  HA1 GLY X   1     -21.476 -67.600  84.661  1.00  0.00      GAG  H
ATOM      7  HA2 GLY X   1     -21.157 -65.997  85.450  1.00  0.00      GAG  H
ATOM      8  C   GLY X   1     -23.103 -66.411  85.215  1.00  0.00      GAG  C
ATOM      9  O   GLY X   1     -23.249 -65.504  84.385  1.00  0.00      GAG  O
ATOM     10  N   ALA X   2     -24.180 -66.939  85.847  1.00  0.00      GAG  N
ATOM     11  HN  ALA X   2     -24.180 -67.788  86.402  1.00  0.00      GAG  H
ATOM     12  CA  ALA X   2     -25.441 -66.230  85.763  1.00  0.00      GAG  C

ATOM      1 N    GLY X   1     -21.525 -67.562  86.759  1.00  1.00      GAG  N  
ATOM      2 HT1  GLY X   1     -22.003 -68.460  86.892  1.00  0.00      GAG  H  
ATOM      3 HT2  GLY X   1     -21.905 -66.929  87.525  1.00  0.00      GAG  H  
ATOM      4 HT3  GLY X   1     -20.492 -67.726  86.876  1.00  0.00      GAG  H  
ATOM      5 CA   GLY X   1     -21.725 -66.910  85.457  1.00  1.00      GAG  C  
ATOM      6 HA1  GLY X   1     -21.476 -67.600  84.661  1.00  0.00      GAG  H  
ATOM      7 HA2  GLY X   1     -21.157 -65.997  85.450  1.00  0.00      GAG  H  
ATOM      8 C    GLY X   1     -23.103 -66.411  85.215  1.00  1.00      GAG  C  
ATOM      9 O    GLY X   1     -23.249 -65.504  84.385  1.00  1.00      GAG  O  
ATOM     10 N    ALA X   2     -24.180 -66.939  85.847  1.00  1.00      GAG  N  
ATOM     11 HN   ALA X   2     -24.180 -67.788  86.402  1.00  0.00      GAG  H  
ATOM     12 CA   ALA X   2     -25.441 -66.230  85.763  1.00  1.00      GAG  C  

Files Used and Created in Example


Case 3: PDB Utilities : Modify PDB Fields

The modify pdb fields pdb utility option has several input fields. Several independent changes can be carried out in a single run. This method is designed to overwrite values in a single canonical PDB ATOM/HETATM field to a single new value based on an atom selection string provided by the user. While many independent changes can be made in one run, a single pdb file is written to disk. Note that the changes are carried on sequentially thus if subsequent field modifications overlap with all or parts of a previous modification then the results may not be what one expects.

The default inputs are shown below.

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Here is an example of modifying an input pdb file where the beta field is set to 1.00 for all atoms with an index < 10.

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Inspecting the first few lines of the original and final pdb files highlights the changes.


ATOM      1  N   GLY X   1     -21.525 -67.562  86.759  1.00  0.00      GAG  N 
ATOM      2  HT1 GLY X   1     -22.003 -68.460  86.892  1.00  0.00      GAG  H
ATOM      3  HT2 GLY X   1     -21.905 -66.929  87.525  1.00  0.00      GAG  H
ATOM      4  HT3 GLY X   1     -20.492 -67.726  86.876  1.00  0.00      GAG  H
ATOM      5  CA  GLY X   1     -21.725 -66.910  85.457  1.00  0.00      GAG  C
ATOM      6  HA1 GLY X   1     -21.476 -67.600  84.661  1.00  0.00      GAG  H
ATOM      7  HA2 GLY X   1     -21.157 -65.997  85.450  1.00  0.00      GAG  H
ATOM      8  C   GLY X   1     -23.103 -66.411  85.215  1.00  0.00      GAG  C
ATOM      9  O   GLY X   1     -23.249 -65.504  84.385  1.00  0.00      GAG  O
ATOM     10  N   ALA X   2     -24.180 -66.939  85.847  1.00  0.00      GAG  N
ATOM     11  HN  ALA X   2     -24.180 -67.788  86.402  1.00  0.00      GAG  H
ATOM     12  CA  ALA X   2     -25.441 -66.230  85.763  1.00  0.00      GAG  C

ATOM      1 N    GLY X   1     -21.525 -67.562  86.759  1.00  1.00      GAG  N  
ATOM      2 HT1  GLY X   1     -22.003 -68.460  86.892  1.00  1.00      GAG  H  
ATOM      3 HT2  GLY X   1     -21.905 -66.929  87.525  1.00  1.00      GAG  H  
ATOM      4 HT3  GLY X   1     -20.492 -67.726  86.876  1.00  1.00      GAG  H  
ATOM      5 CA   GLY X   1     -21.725 -66.910  85.457  1.00  1.00      GAG  C  
ATOM      6 HA1  GLY X   1     -21.476 -67.600  84.661  1.00  1.00      GAG  H  
ATOM      7 HA2  GLY X   1     -21.157 -65.997  85.450  1.00  1.00      GAG  H  
ATOM      8 C    GLY X   1     -23.103 -66.411  85.215  1.00  1.00      GAG  C  
ATOM      9 O    GLY X   1     -23.249 -65.504  84.385  1.00  1.00      GAG  O  
ATOM     10 N    ALA X   2     -24.180 -66.939  85.847  1.00  0.00      GAG  N  
ATOM     11 HN   ALA X   2     -24.180 -67.788  86.402  1.00  0.00      GAG  H  
ATOM     12 CA   ALA X   2     -25.441 -66.230  85.763  1.00  0.00      GAG  C  

Files Used and Created in Example


Case 4: PDB Utilities : Translate/Rotate

The translate/rotate pdb utility option can be used to alter the coordinates (x, y, z) of the structure provided by the input pdb file. Translation and rotation operations can be done separately or together. Note that only a single final structure exists for each run. Rotation operations use the right-handed coordinate system.

The default inputs are shown below.

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user vector: rotation about user supplied vector. This selection provides additional input.

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Here is an example of modifying an input pdb file where the molecule is pre-centered at [0,0,0], then translated to [20.0, 13.6, 0.0] and rotated about the cardinal x axis by 90 degrees.

Inspecting the first few lines of the original and final pdb files highlights the changes.


ATOM      1  N   GLY X   1     -21.525 -67.562  86.759  1.00  0.00      GAG  N 
ATOM      2  HT1 GLY X   1     -22.003 -68.460  86.892  1.00  0.00      GAG  H
ATOM      3  HT2 GLY X   1     -21.905 -66.929  87.525  1.00  0.00      GAG  H
ATOM      4  HT3 GLY X   1     -20.492 -67.726  86.876  1.00  0.00      GAG  H
ATOM      5  CA  GLY X   1     -21.725 -66.910  85.457  1.00  0.00      GAG  C
ATOM      6  HA1 GLY X   1     -21.476 -67.600  84.661  1.00  0.00      GAG  H
ATOM      7  HA2 GLY X   1     -21.157 -65.997  85.450  1.00  0.00      GAG  H
ATOM      8  C   GLY X   1     -23.103 -66.411  85.215  1.00  0.00      GAG  C
ATOM      9  O   GLY X   1     -23.249 -65.504  84.385  1.00  0.00      GAG  O
ATOM     10  N   ALA X   2     -24.180 -66.939  85.847  1.00  0.00      GAG  N
ATOM     11  HN  ALA X   2     -24.180 -67.788  86.402  1.00  0.00      GAG  H
ATOM     12  CA  ALA X   2     -25.441 -66.230  85.763  1.00  0.00      GAG  C

ATOM      1 N    GLY X   1       5.266 -65.093 -43.846  1.00  0.00      GAG  N  
ATOM      2 HT1  GLY X   1       4.788 -65.226 -44.744  1.00  0.00      GAG  H  
ATOM      3 HT2  GLY X   1       4.886 -65.859 -43.213  1.00  0.00      GAG  H  
ATOM      4 HT3  GLY X   1       6.299 -65.210 -44.010  1.00  0.00      GAG  H  
ATOM      5 CA   GLY X   1       5.066 -63.791 -43.194  1.00  0.00      GAG  C  
ATOM      6 HA1  GLY X   1       5.315 -62.995 -43.884  1.00  0.00      GAG  H  
ATOM      7 HA2  GLY X   1       5.634 -63.784 -42.281  1.00  0.00      GAG  H  
ATOM      8 C    GLY X   1       3.688 -63.549 -42.695  1.00  0.00      GAG  C  
ATOM      9 O    GLY X   1       3.542 -62.719 -41.788  1.00  0.00      GAG  O  
ATOM     10 N    ALA X   2       2.611 -64.181 -43.223  1.00  0.00      GAG  N  
ATOM     11 HN   ALA X   2       2.611 -64.736 -44.072  1.00  0.00      GAG  H  
ATOM     12 CA   ALA X   2       1.350 -64.097 -42.514  1.00  0.00      GAG  C  

The operations are visualized in the images below.


>>> m1.calccom(0)
array([ -6.79114736, -23.71577133,   8.06558513])


>>> m2.calccom(0)
array([  1.99998526e+01,   1.36004149e+01,   2.28664870e-04])


Files Used and Created in Example


Cases 5 & 6: PDB Utilities : Align On PMI

The align on pmi pdb utility option can be used to alter the coordinates (x, y, z) of the structure provided by the input pdb file. There are options to align the principal moments of inertia on a single axis or to align all three principal moments of inertia on cardinal axes (x,y,z). Note that only a single final structure exists for each run. Rotation operations use the right-handed coordinate system.

The default inputs are shown below.

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As stated above, if one chooses align pmi to cardinal axes in the choose axis/axes listbox selection then there are no further input options.

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Two examples will be highlighted.

(1) An example of modifying an input pdb file where the prinicpal moments of inertia are aligned on the cardinal axes.

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Inspecting the first few lines of the original and final pdb files highlights the changes.


ATOM      1  N   GLY X   1     -21.525 -67.562  86.759  1.00  0.00      GAG  N 
ATOM      2  HT1 GLY X   1     -22.003 -68.460  86.892  1.00  0.00      GAG  H
ATOM      3  HT2 GLY X   1     -21.905 -66.929  87.525  1.00  0.00      GAG  H
ATOM      4  HT3 GLY X   1     -20.492 -67.726  86.876  1.00  0.00      GAG  H
ATOM      5  CA  GLY X   1     -21.725 -66.910  85.457  1.00  0.00      GAG  C
ATOM      6  HA1 GLY X   1     -21.476 -67.600  84.661  1.00  0.00      GAG  H
ATOM      7  HA2 GLY X   1     -21.157 -65.997  85.450  1.00  0.00      GAG  H
ATOM      8  C   GLY X   1     -23.103 -66.411  85.215  1.00  0.00      GAG  C
ATOM      9  O   GLY X   1     -23.249 -65.504  84.385  1.00  0.00      GAG  O
ATOM     10  N   ALA X   2     -24.180 -66.939  85.847  1.00  0.00      GAG  N
ATOM     11  HN  ALA X   2     -24.180 -67.788  86.402  1.00  0.00      GAG  H
ATOM     12  CA  ALA X   2     -25.441 -66.230  85.763  1.00  0.00      GAG  C


ATOM      1 N    GLY X   1      -7.307   1.292  90.979  1.00  0.00      GAG  N  
ATOM      2 HT1  GLY X   1      -7.565   0.513  91.594  1.00  0.00      GAG  H  
ATOM      3 HT2  GLY X   1      -7.857   2.127  91.342  1.00  0.00      GAG  H  
ATOM      4 HT3  GLY X   1      -6.270   1.446  91.073  1.00  0.00      GAG  H  
ATOM      5 CA   GLY X   1      -7.600   1.111  89.550  1.00  0.00      GAG  C  
ATOM      6 HA1  GLY X   1      -7.162   0.184  89.202  1.00  0.00      GAG  H  
ATOM      7 HA2  GLY X   1      -7.262   1.987  89.027  1.00  0.00      GAG  H  
ATOM      8 C    GLY X   1      -9.045   1.091  89.208  1.00  0.00      GAG  C  
ATOM      9 O    GLY X   1      -9.365   1.377  88.046  1.00  0.00      GAG  O  
ATOM     10 N    ALA X   2      -9.993   0.743  90.112  1.00  0.00      GAG  N  
ATOM     11 HN   ALA X   2      -9.817   0.329  91.021  1.00  0.00      GAG  H  
ATOM     12 CA   ALA X   2     -11.381   1.004  89.787  1.00  0.00      GAG  C  

(2) An example of modifying an input pdb file where the first prinicpal moment of inertia (I1) is aligned along the z-axis and moved so that the molecule lies on the x-y plane (all z-coordinates > 0).

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Inspecting the first few lines of the original and final pdb files highlights the changes. Note in both visualizations the origin is at the intersection of the red (x axis), green (y axis) and blue (z axis) with the head of the arrows indicating positive values.


ATOM      1  N   GLY X   1     -21.525 -67.562  86.759  1.00  0.00      GAG  N 
ATOM      2  HT1 GLY X   1     -22.003 -68.460  86.892  1.00  0.00      GAG  H
ATOM      3  HT2 GLY X   1     -21.905 -66.929  87.525  1.00  0.00      GAG  H
ATOM      4  HT3 GLY X   1     -20.492 -67.726  86.876  1.00  0.00      GAG  H
ATOM      5  CA  GLY X   1     -21.725 -66.910  85.457  1.00  0.00      GAG  C
ATOM      6  HA1 GLY X   1     -21.476 -67.600  84.661  1.00  0.00      GAG  H
ATOM      7  HA2 GLY X   1     -21.157 -65.997  85.450  1.00  0.00      GAG  H
ATOM      8  C   GLY X   1     -23.103 -66.411  85.215  1.00  0.00      GAG  C
ATOM      9  O   GLY X   1     -23.249 -65.504  84.385  1.00  0.00      GAG  O
ATOM     10  N   ALA X   2     -24.180 -66.939  85.847  1.00  0.00      GAG  N
ATOM     11  HN  ALA X   2     -24.180 -67.788  86.402  1.00  0.00      GAG  H
ATOM     12  CA  ALA X   2     -25.441 -66.230  85.763  1.00  0.00      GAG  C


ATOM      1 N    GLY X   1      65.406 -63.253  29.423  1.00  0.00      GAG  N  
ATOM      2 HT1  GLY X   1      65.293 -64.239  29.682  1.00  0.00      GAG  H  
ATOM      3 HT2  GLY X   1      66.252 -62.917  29.973  1.00  0.00      GAG  H  
ATOM      4 HT3  GLY X   1      65.582 -63.209  28.386  1.00  0.00      GAG  H  
ATOM      5 CA   GLY X   1      64.265 -62.373  29.716  1.00  0.00      GAG  C  
ATOM      6 HA1  GLY X   1      63.365 -62.785  29.278  1.00  0.00      GAG  H  
ATOM      7 HA2  GLY X   1      64.513 -61.382  29.379  1.00  0.00      GAG  H  
ATOM      8 C    GLY X   1      64.009 -62.146  31.161  1.00  0.00      GAG  C  
ATOM      9 O    GLY X   1      63.388 -61.123  31.481  1.00  0.00      GAG  O  
ATOM     10 N    ALA X   2      64.404 -63.030  32.109  1.00  0.00      GAG  N  
ATOM     11 HN   ALA X   2      64.757 -63.965  31.933  1.00  0.00      GAG  H  
ATOM     12 CA   ALA X   2      64.358 -62.615  33.497  1.00  0.00      GAG  C  

Files Used and Created in Examples


Fasta Utilities Options

Case 7: Fasta Utilities

The fasta utilities option can be used to generate a mock sequence pdb file that can be used to build complete structures. Typically one uses two pdb files to create a complete molecule using the program psfgen (provided by the NAMD group). One pdb contains only atoms with known coordinates and a second "sequence" pdb with at least one atom per residue for the entire structure including atoms for which coordinates do not exist. Using these two pdb files and the psfgen program, one can patch small regions of otherwise missing atoms in the full structure.

The default inputs are shown below.

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Here is an example of converting a protein sequence FASTA file to a mock sequence pdb file.

Inspecting the original fasta sequence file and final pdb files highlights the changes.


> this is a test
RRGTWPFGAAA

ATOM      1 CA   ARG A   1       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM      2 CA   ARG A   2       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM      3 CA   GLY A   3       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM      4 CA   THR A   4       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM      5 CA   TRP A   5       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM      6 CA   PRO A   6       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM      7 CA   PHE A   7       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM      8 CA   GLY A   8       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM      9 CA   ALA A   9       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM     10 CA   ALA A  10       0.000   0.000   0.000  0.00  0.00      DUM  C  
ATOM     11 CA   ALA A  11       0.000   0.000   0.000  0.00  0.00      DUM  C  
END

Files Used and Created in Example


Reference(s) and Citations

  1. NAMD User Guide

  2. FASTA

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