Methods to modify PDB files and structures to help build starting structures for modeling.
The Build Utilities module is accessible from the Beta section of the main menu.
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.
If your input pdb file has multiple models or frames, only the first frame is modified and written to a new pdb file.
All methods will result in a new pdb file that will be written to the user supplied run name + build_utilities directory located in the active project directory.
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
PDB utilities requires an input pdb file and to select one of the modification options.
pdb file input: name of pdb file to read in and to modify using one of the pdb utilities methods
select pdb utitity option: user can choose one of the following options:
renumber indices/residues: to renumber indices and/or residue numbers for entire pdb file
make constraint file(s): to alter either occupancy or beta fields for specific selections
modify pdb fields: to alter any number of standard pdb fields to a single value based on user selection
translate/rotate: to alter coordinates by performing user supplied translation and rotation options
align on pmi: to alter coordinates by aligning input structure on pmi axis or axes
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.
The renumber indices/residues pdb utility option has several input fields.
One or both of the following checkboxes must be selected:
renumber indices: check box to indicate that indices should be renumbered.
enter index of first atom: new integer value of the first atom index in be written to file
renumber residue numbers: check box to indicate that residue numbers should be renumbered.
enter index of first residue: new integer value of the first residue index in be written to file.
Indices and/or residue numbers will increment for each atom and/or residue in the entire file starting with the user
supplied value(s).
Here is an example of renumbering an input pdb file where the indices are renumbered from 23 and residue numbers from 47.
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
input files
output files
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.
number of constraint pdb files to create: integer selection must be greater or equal to 1. If a value greater than 1 is selected then the following options will be required for each desired constraint pdb file.
select option:
heavy atoms: all non-hydrogen atoms.
protein: atoms in protein residues.
nucleic: atoms in residues ADE, GUA, THY, CYT or URA. NOT YET IMPLEMENTED
backbone: atoms representing the single chain biopolymer backbone (e.g. protein N, CA, C, O atoms).
solute: all non water components. NOT YET IMPLEMENTED
select field to hold value: one of the following two options can be selected.
occupancy: columns 55-60 in pdb file
beta: columns 61-66 in pdb file
reset all values to zero: checkbox, that if selected, will set all selected field values to zero before setting the appropriate values to 1.00
name of constraint pdb file: name of modified pdb file to be written to disk.
Here is an example of modifying an input pdb file where the beta field is set to 1.00 for heavy atoms (non-hydrogen).
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
input files
output files
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.
output pdb file name: name of modified pdb file to be written to disk.
number of field modifications: integer selection must be greater than or equal to 1. If a value greater than 1 is selected then the following options will be required for each desired modification to the original pdb file.
selection: unique logical selection string to identify atoms that will be chosen to modify a user selected field (VMD like input).
field to modify: a list of canonical pdb atom record fields. One field can be chosen for each desired field modification. The name of the field is followed by a description contained in brackets that indicates the number of allowed characters and the required data type. The data types allowed are ascii (alphanumeric), float and integer.
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.
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
input files
output files
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.
output pdb file name: name of modified pdb file to be written to disk.
pre-center coordinates at [0,0,0]: optional checkbox to move the center of mass of the molecule to x=0, y=0 and z=0.
x translation: float value of desired translation in the x-dimension (angstroms).
y translation: float value of desired translation in the y-dimension (angstroms).
z translation: float value of desired translation in the z-dimension (angstroms).
choose axis of rotation: optional listbox selection to perform rotation operations.
none: no rotation operations will be carried out.
cardinal axes: rotation about cardinal axes (x,y,z). This selection provides additional input.
theta x rotation: angle (degrees).
theta y rotation: angle (degrees).
theta z rotation: angle (degrees).
user vector: rotation about user supplied vector. This selection provides additional input.
choose order of rotation operations: select the order of rotation operations. If a specific rotation axis is not desired then enter "0" degrees in the appropriate theta rotation below.
user supplied vector: user supplied list comma separated floats to define the rotation axis. The origin of this vector is [0,0,0].
theta x rotation: angle (degrees).
theta y rotation: angle (degrees).
theta z rotation: angle (degrees).
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])
input files
output files
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.
output pdb file name: name of modified pdb file to be written to disk.
choose axis/axes: select alignment option to either align a single principal moment of inertia to a single axis or to align all three principal moments of inertia to cardinal axes (x,y,z). The first option has further input parameters.
choose pmi axis: I1, I2, or I3. Principal moments are calculated from the user supplied structure in the intial pdb file and sorted from highest (I1) to lowest (I3).
choose alignment vector to align to: Axis to align chosen pmi axis. Values include cardinal axes (x,y,z) or usser supplied vector. If chosen then the following single input field is provided.
select to move molecule to a surface plane: This is an optional checkbox to indicate that the molecule is moved following alignment along the alignment axis such that all atoms have coordinates in that axis greater than the supplied value. This is useful, as an example, to align a principal moment on the z-axis and then move the molecule along the z-axis so all values are greater than 0.0, thus modeling the surface as the x-y plane with the molecule sitting on this plane with all z-coordinates greater than zero.
rotate molecule 180 degrees prior to moving to surface: A checkbox to allow one to essentially flip the molecule upside down along the alignment axis if required to orient it properly if it turns out the principal moment vector happens to point in the opposite direction.
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.
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.
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).
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
input files
output files
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.
output pdb file name: name of modified pdb file to be written to disk.
select molecule type: only protein and nucleic acids sequences are supported.
select option: Two choices:
enter fasta sequence: by pasting into the supplied text area.
upload fasta sequence file: from a properly formmated fasta file.
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
input files
output files
Supported via CCP-SAS a joint EPSRC (EP/K039121/1) and NSF (CHE-1265821) grant