iMODFIT Linux64

  • Last update: 06 March 2017
  • File size: 16.99 MB
  • Version: 1.44
  • Downloaded: 106
  • Author: Lopez-Blanco JR and Chacon P.
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#      iMODFIT 1.44 (from release v1.06)                                               #
#      Chacon's lab - May 10th, 2016                                                     #
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In this release (v1.06), the last stable version of iMODFIT (v1.44) is provided.
It is intended to work, but testing is very limited.


------------------------------------------------------------
iMODFIT v1.44 (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           v1.44 --> Flexible fitting tool.
pdb2vol           v1.01 --> Simulated maps generation from PDB files.
rmsd              v1.03 --> Optimal atomic structures alignment (RMSD min.).
pdb               v0.99 --> 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 only tested with 64-bit Intel "icpc"
(v. 13.0.1) and GNU "gcc" (4.6.3) compilers.

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
13.0.1 (gcc version 4.6.0 compatibility).

Please, download and install the Intel C++ Compiler and Math Kernel Library:
  "Intel C++ Composer XE for Linux" (current tested version is 2013.1.117)
 
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 v1.44 IMPROVEMENTS
--------------------------

The main improvements with respect to the previous version are:

1) Improved stability for very big and/or symmetrical macromolecular complexes.

2) 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.

3) Improved default parameters.

4) 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 v1.44 TEST
------------------

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)