ADPEM Linux64

  • Last update: 28 February 2019
  • File size: 11.60 MB
  • Version: 2.1
  • Downloaded: 269
  • Author: Garzon JI, Kovacs JA, Abagyan R, and Chacon P.
5.0/5 rating (2 votes)

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# --- ADPEM 2.1 (from release v1.07)     --- #
# --- Chacon's lab - Feb 28th, 2019      --- #
##############################################

The last stable version of ADPEM (v2.1) is released with
a beta-version of ADPEM_OPT (v0.9) and other EM tools.


--------------------------------------------------------
ADP_EM (Another Docking Program for Electron Microscopy)
--------------------------------------------------------

We provide LINUX statically linked 64-bit executables generated with Intel and
GNU compilers to minimize library dependence problems.

> Programs provided
-------------------
adpem v2.1 --> Exhaustive 6D rigid body fitting.
adpem_opt v0.9 --> Local rigid (multi-)body fitting (off-grid).
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 released
-------------------

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

* 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).


-------------------
ADP_EM IMPROVEMENTS
-------------------

Main improvements of v2.1 with respect to previous (v1.04) are:

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

Main improvements of v1.04 with respect to previous (v1.0) are:

- Improved map handling.
- Minor bugs removed.


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

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

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

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


--------------
ADPEM EXAMPLES
--------------

We have included two simple test cases in the adpem_test/ subdirectory.
Please, just follow the instructions:

> Simple ADPEM tests
--------------------

FILES:

chainA.pdb extracted from 2C7E.pdb
chainH.pdb extracted from 2C7E.pdb
emd1047.ccp4 downloaded from EMD,
remove discontinuous density
using voledit tool od SITUS package
(floodfill at 0.060)

ringA-G.pdb (heptameric ring chains from A to G of 2C7E.pdb)
ringH_N.pdb heptameric ring chains from H to N of 2C7E.pdb)

resolution 14.9 cutoff 0.060

To run the program go to the adpem_test/ directory:

1) fit chainA into GROEL-ATP map

../bin/adp_em emd1047.ccp4 chainA.pdb 16 0.060 14.9 -n 20

ringA-G_docked.pdb was build by integrating the first 7 best solutions found

2) fit chainH into GROEL-ATP map

../bin/adp_em emd1047.ccp4 chainH.pdb 16 0.060 14.9 -n 20

ringH-N_docked.pdb was build by integrating the first 7 best solutions found

In directories chainH/ and chainA/ you can find the results
performed in a linux box with an intel Intel(R) Core(TM) i7 CPU 950 3.07GHz
(includes a log file of the screen output of the respective runs)

*More accurate (but slower) results can be obtained using higher bandwidths,
e.g. 32 instead of 16.


> Simple ADPEM_OPT tests
------------------------

The following two examples suffice to illustrate the adpem_opt usage:

1) Multiple fit of the 7 monomers (one ring) that were fitted before in adpem.

cd chainA/
../../bin/adpem_opt ../emd1047.ccp4 0.065 14.9 adpEM0001.pdb adpEM0002.pdb adpEM0003.pdb adpEM0004.pdb adpEM0005.pdb adpEM0008.pdb adpEM0020.pdb

The refined poses are named adpEMopt000X.pdb. Note that all poses are better
fitted to the density, particularly, adpEMopt0003.pdb and adpEMopt0007.pdb.

2) Multiple fit of 2 monomers (the worst fitted) while fixing the others.

cd chainA/
../../bin/adpem_opt ../emd1047.ccp4 0.065 14.9 adpEM0003.pdb adpEM0020.pdb --fixed adpEM0001.pdb,adpEM0002.pdb,adpEM0004.pdb,adpEM0005.pdb,adpEM0008.pdb -o mul
tifix

Only the not fixed pdbs, multifix0001.pdb multifix0002.pdb, were fitted.
To prevent overwritting issues, the basename ("multifit") was added.


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

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

Garzon JI, Kovacs JA, Abagyan R, and Chacon P. (2007) ADP_EM: Fast exhaustive
multi-resolution docking for high-throughput coverage. Bioinformatics.
23(4):427-33.


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

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

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


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