iMODFIT Linux64

  • Last update: 28 February 2019
  • File size: 7.09 MB
  • Version: 1.51
  • Downloaded: 349
  • Author: Lopez-Blanco JR and Chacon P.
5.0/5 rating (5 votes)

###############################################
# --- iMODFIT 1.51 (from release v1.07)   --- #
# --- Chacon's lab - Feb 28th, 2019       --- #
###############################################

The last stable version of iMODFIT (v1.44) is released with
other EM tools.


-------------------------------------------------------
iMODFIT (Internal coordinates normal MODe based FITing)
-------------------------------------------------------

We provide 64-bit LINUX statically linked executables generated with GNU
compilers to minimize library dependence problems. Dynamic linking was used
for the faster Intel Math Kernel Library (MKL) version.

> Programs provided
-------------------
imodfit v1.51 --> Flexible fitting tool.
pdb2vol v1.01 --> Simulated maps generation from PDB files.
rmsd v1.04 --> Optimal atomic structures alignment (RMSD min.).
pdbtool v1.01 --> Atomic structures manipulation tool.

*All the programs show a basic help text using the --help option.

> Binaries releases
-------------------

Pre-compiled binaries are available in the corresponding bin/ directory. You
can choose the appropriate release for your system:

[Program] Compiler Libraries Linkage
-----------------------------------------------------------
*<TOOL> Intel icpc - static
<TOOL>_gcc GNU gcc - static
*<TOOL>_mkl Intel icpc MKL dynamic

* Intel compiled binaries are the fastest alternatives.
<TOOL> corresponds to the name of the program.


------------
REQUIREMENTS
------------

This software release has been compiled with 64-bit Intel "icpc"
(v. 19.0.2.187) and GNU "gcc" (7.3.0).

Statically linked executables are ready-to-use (nothing else required).

The following libraries may be required only to run the pre-compiled binaries
of the Intel MKL release:

- Intel's C++ Compiler and Math Kernel Library - Current tested icpc version
19.0.2.187 (gcc version 7.3.0 compatibility).

Please, download and install the Intel C++ Compiler and Math Kernel Library:
"Intel C++ Parallel Studio XE 2019 update-2 for Linux" (current tested
version is 19.0.2.187)

Newer Intel MKL versions should work as well.

Intel C++ Compiler and MKL libraires can be obtained for from Intel's web site:
http://software.intel.com/en-us/articles/non-commercial-software-download/


--------------------
iMODFIT IMPROVEMENTS
--------------------

The main improvements of v1.51 with respect to the previous (v1.44) are:

- Integration with Chimera's plug-in.
- Minor bugs removed.

The main improvements with respect to older versions are:

- Improved stability for very big and/or symmetrical macromolecular complexes.
- Improved speed thanks to our new parallel band-Krylov eigensolver:
Aliaga JI, Alonso P, Badia JM, Chacon P, Davidovic D, Lopez-Blanco JR, and Quintana-Orti ES
(2016). A fast band-Krylov eigensolver for macromolecular functional motion simulation on
multicore architectures and graphics processors. Journal of Computational
Physics 309:314-323.
- Improved default parameters.
- Minor bugs removed.


--------
TUTORIAL
--------

We encourage you to visit our web site and follow the tutorials:

http://chaconlab.org/methods/fitting/imodfit/imodfit-tuto

*Some files to be used in the tutorial can be found in the imodfit_test/
directory.


---------------
iMODFIT EXAMPLE
---------------

We have included a simple test case in the imodfit_test/ subdirectory.

The basic flexible fitting procedure is very simple. Please, just copy and
paste the following commands in your terminal:

Go to the test directory
$ cd imodfit_test

Perform the basic flexible fitting with a 10A target map
$ ../bin/imodfit_mkl 1sx4A.pdb 1oel.ccp4 10 0 -t

Check iMODFIT performance by directly visualizing the fitting movie
(imodfit_movie.pdb) in your favorite viewer (VMD works fine).

Alternatively, compute the C-alpha RMSD between the fitted model and the PDB
employed to simulate the target map:
$ ../bin/rmsd imodfit_fitted.pdb 1oel.pdb -c

The final C-alpha RMSD is just 1.3752 A (1.2098 A after optimal alignment).

You can try the flexible fitting in the opposite direction:
$ ../bin/imodfit_mkl 1sx4A.pdb 1oel.ccp4 10 0 -t

The complete test takes around 13/8 minutes for gcc/intel binaries using an
Intel(R) Core(TM) i7 CPU 950 running at 3.07GHz.


----------
REFERENCES
----------

Please, cite our work if any of our tools become useful for your research.

iMODFIT: Efficient and robust flexible fitting based on vibrational analysis
in internal coordinates (2013). Lopez-Blanco JR and Chacon P. JSB
184(2):261-270.


-------
CONTACT
-------

Please, feel free to contact with us!
(Any suggestion or bug report is welcome)

Jose Ramon Lopez-Blanco (PhD.)
jrlopez(at)iqfr.csic.es

Pablo Chacon (PhD.)
pablo(at)chaconlab.org


Structural Bioinformatics Group
IQFR-CSIC - Madrid (Spain)
(http://chaconlab.org)