This software performs trilateration using an arbitrary number of donor sites
and FRET distances with the aim to locate the position of a FRET acceptor in a
protein structure. Our trilateration approach takes into account Gaussian
distance distributions as fitted to the FLT-FRET measurement for each donor
position. The normalized sum of the distance distributions from all of the
donor sites to one acceptor is generated as a probability map describing the
acceptors location. This volumetric map is saved in MRC/CCP4-format, which
can be displayed using common molecular graphics software.
The code is written in fortran and follow the Fortran 2003 standard. Source code
file is, trilat-umn.f03, which can be compiled using the gfortran compiler
using the following command line:
> gfortran -o trilat trilat-umn.f03
Compilation is fast and takes just seconds on most modern computers.
The software is intended to be run from a command line, preferentially a Linux shell.
The executable has been tested on several Linux systems and on the Cygwin
environment in Windows. The software has no additional hardware or software requirements.
The software runs in seconds and writes an output file which is a probability density
map in the MRC/CCP4 format. The file size is typically 50-300MB depending on input data.
Usage: trilat [-h | -v | -g | -x] [-r RESOL | -a FACTOR | -m FACTOR] datafile
options:
-v, --version print version information and exit
-h, --help print usage information and exit
-r, --resol set resolution/grid spacing [1.0]
-g, --gauss input file contains Center positions and FWHM for Gaussians
-x, --minmax input file contains range specification with Min and Max distances
-q, --quad adds a quadratic function on flanks of Min/Max data
-a, --add FACTOR factor to add/subrtract to adjust width
-m, --mult FACTOR factor to multiply to adjust width
-e, --negprob shifts flanks of distance distributions to be negative (-0.5 to 1)
-n, --n1comb also calculate results for for all combinations of n-1 distances
Example:
> trilat -g input.dat
Output:
trilat by Bengt Svensson, BMBB, UMN, USA.
Reading from file: input.dat
Number of distances: 5
Number of sites: 5
Writing to file: input_R1_14_32_44_49_85.mrc
trilat completed successfully.
The -q, -a, -m, and -e flags are for testing purposes only.
It is recommended to use the software with Gaussian distance distribution. For that
an input data file should have the following format:
14 112.201 202.504 274.899 60.02 21.29 1.0 62.0 4.1
32 150.696 226.353 302.045 46.15 35.24 1.0 62.0 4.1
44 133.711 210.394 260.188 55.36 21.37 1.0 62.0 4.1
49 136.318 195.050 272.275 50.28 20.57 1.0 62.0 4.1
85 156.203 207.390 296.140 34.92 36.95 1.0 62.0 4.1
Where the column 1 lists residue number,
column 2-4 list x, y, z coordinates for the acceptor location,
column 5 center position for the Gaussian fit,
column 6 FWHM for the fit,
column 7 a scaling factor to weigh the individual sets,
column 8 R0 for the probe pair,
column 9 lifetime for the acceptor
When using MinMax instead of Gaussian fits, columns 5 is Min,
and column 6 is Max distance.
For any questions about this software please contact Bengt Svensson at
svens005@umn.edu
The trilat-umn software trilaterates a location in space based on FRET
distances.
Copyright (C) 2018 Bengt Svensson
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
