Facio

3D-Graphics program for
Molecular Modeling
and
Visualization of Quantum Chemical Calculations

Current Version (released on March 14, 2010)

Facio 14.2.3 Full Package (14.2MB)
Facio 14.2.3_Update  (2.84MB) 

Although Facio is a native application of Windows environment, it is perfectly working on Linux
with a help of WINE and Mesa,
and on Macintosh (Intel Mac) with VMWare Fusion,
CrossOver Mac, or Darwine.
 　　 C1280

  Message Digest of the distributing ZIP archive (Full Package)
MD5  :03bdb30c70af76bbb0eded72ff4af632
SHA-1:058904d7d01c4d4171c0ec1379f99555531ef0be                                                    Japanese Page

Facio 11.8.2 and 11.8.3 are minor bug fix versions of Facio 11.8.1 and 11.8.2, respectively.
The new feature of Facio 11.8.1  :  Point Mutation of Protein and Function to Show Intermediate Structures
                                                     of Optimization/Transition State Search Calculation of GAMESS/Gaussian.
The new feature of Facio 11.7.1  :  2D Map Representation of Two-Body FMO Properties
                                                     and Rainbow Fragment
Facio 11.6.2 is a minor bug fix version of Facio 11.6.1.
The new feature of Facio 11.6.1  :  PDB Utilities
The new feature of Facio 11.5.1  :  Upgrade of PIEDA panel
 The new feature of Facio 11.4.1  :  PIEDA and Half transparent representation
The new feature of Facio 11.1.1  :  GUI for FMO and Local Structure Viewer

Up to 20 molecular orbitals can be viewed simultaneously. (See the screen shot below)
The movement of the molecule in each sub window is synchronized with that of the main window.

Facio is an OpenGL-based 3D-graphics program for molecular modeling and visualization of quantum chemical calculations (GAMESS and Gaussian).
SSH / SFTP client is also implemented. Through SSH / SFTP connection, Gaussian job can be submitted to batch job system on the remote server and calculation results can be retrieved form the server. Supported batch job systems are LoadLeveler and NQS.
Since Facio internally uses PDB (Protein Data Bank) format, it can also display a 3D-structure of biological macromolecules, such as proteins and nucleic acid with emphasizing their secondary or quaternary structures.

-- Note --
Facio is tested on Windows 98SE, Me, NT, 2000 and XP.
But it is reported that sometimes Facio does not work properly.

In that case, follow the instructions below to disable or constrain 3D graphics accleration.

(1) Click on the Start Menu\Settings\Control Panel shortcut.
(2) Double click on the System Icon, in the Control Panel.
(3) Click on the Performance Tab in the System Properties Dialog.
(4) Click on the Graphics button in the Performance tab.
(5) Either slide the acceleration to NONE, or Level 1.

And make sure you have downloaded and installed the latest drivers for your graphics card.
If it does not help, try to update your DirectX too.

1. Molecular Modeling Features

Modeling is simple. Replacing a hydrogen with CH3, CH2, CH, Phenyl, OH, Formyl, NH2 and Glycosyl, molecular model is assembled. Besides ordinary functions required for molecular modeling, Facio featues the following functions.
  1. Geometry Optimization with PC GAMESS or WinGamess
  2. Rendezvous and Docking of Two Molecules
    ([5]circulene and [7]circulene in this example)
  • Two molecular files (in PDB format) can be successively loaded.
  • And the relative position of the latter molecule can be adjusted.
  • Any two bonds of each two molecule can be aligned.
  • Two hydrogen atoms are deleted.
  • Making a bond.
  • Group can be moved along the bond.
GIF animation illustrates the rendezvous and docking process. 		　

With Facio, you can make a model of a large and complex molecule, such as Ciguatoxin, a marine natural product. Final structure of Ciguatoxin and their modeling intermediates are available in PDB foramt. Ciguatoxin.exe (self-extracting archives)
Ciguatoxin

2. Visualization of Quantum Chemical Calculations

　　　 Molecular Orbital of Naphthalene's HOMO

Facio can visualize CUBE Molecular Orbital data of PC GAMESS and Gaussian.
　　　 Normal Mode of Vibration of Benzene shown as a GIF animation.

Facio reads GAMESS punch file or Gaussian output file for normal mode of vibration to display it as an animation ,which is more animated than those shown here.
　　　
Electrostatic Potential mapped on Solvent Excluded Surface

　　　
Electron Density of Water at isovalue of 0.065.

 　　　 Electrostatic Potentials of Water at isovalue of +0.052 and -0.052.
After the version 6.0.1, interface to PC GAMESS supports Saddle Point search and IRC calculation.
IRC data is visualized for PC GAMESS and Gaussian.

After version (6.5.1), IR spectrum can be simulated with IR intensities calculated by GAMESS.

3. Viewing Biological Macromolecule

Facio's native molecular structure format is PDB (Protein Data Bank). Thus, protein or nucleic acid data in PDB format is loadable to Facio. In the former version, Facio sometimes collapsed with fatal exception. This fatal bug has been fixed for the latest version. However, there still exist PDB files that Facio cannot parse.

Example shown below is "Human Transferrin Receptor Protein" (PDB ID: 1CX8).
This protein consists of 8 polymer chains (or subnunits) and this can be easily seen by colored quaternary structure representation. Secondary structures can also be shown by color.

PDB ID: 1CX8 　 PDB ID: 1CX8
Colored by quaternary structure 　 Secondary Structure (Red: Helix, Yellow: Sheet)

4. Viewing Solvent Excluded Surface
Solvent Excluded Surface 　 Solvent excluded surface of Tryptophan
calculated by MSMS as an external program

(Reference to MSMS)
Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) Reduced surface:
an efficient way to compute molecular surfaces. Biopolymers, Vol. 38.,
(3), 305-320.

http://www.scripps.edu/~sanner

5. Building Polypeptide

Specifying secondary structural feature for each amino residue,
polypeptide model is easily built from scratch.
Alpha Helix 　 Beta Turn
Alpha helix 　 Beta turn

6. Building Polysaccharide
Stachyose 　 16 x 2 glycosyl groups derived from 8 x 2 pyranoses and 8 x 2 furanoses are available as substituent.
Oligosaccharide "Stachyose" 　

7. Building Polynucleotide
DNA 　 Polynucleotide model is built from scratch with a help of Tinker (nucleic.exe).
Because of bugs in "nucleic.exe" module collision will occur in Z-form strand.
DNA : B-form double helix of d(AGCTAGCTAGCT) 　

8. Author

Facio was developed at Kyushu University by Masahiko Suenaga.
Comments, suggestions and bug reports are welcome.
visits since Sept. 12, 2004 Logo To Top Page (in Japanese)