Graphite - LifeExplorer: easy DNA modeling

(INRIA / Fondation Fourmentin-Guilbert)

(Graphite/MicroMegas has a new name: Graphite - LifeExplorer)
Biologists need simple spatial modeling tools to help in understanding the role of objects' relative position in the functioning of the cell. In this context, we offer a tool for easy DNA modeling. The tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB.

The manual · I have a problem! · What's new? · I want the software! · Tutorials · Who made this?

Follow @GraphiteLifeExp

Using Graphite - LifeExplorer (G-LE)

You can see videos of G-LE in action here.

A presentation of G-LE and its user manual are available as a PDF file.

A guide on the basic usage of Graphite is avaialable as a PDF file.

A set of tutorials is available.

There is a mailing-list for user help and announces: Check this link to subscribe or see the list's archive.

Troubleshooting

There is a mailing-list for user help and announces: Check this link to subscribe or see the list's archive.
There is a problem tracker for G-LE here. You will have to log in first (and therefore have an account on INRIA's gforge: anyone can create one). Note: If you click on one item in the problem tracker, you access a details page, which may contain comments to the problem, so this tracker may also serves as a FAQ.
You may also contact me. (Also my skype id is samuelhornus.)

News

2012

July 31. Bux fix for quadratic curves, Windows version.
July 30.
- Internal redesign and bug fixes. You will probably not be able to load .elin and .gsg files containing quadratic or cubic Bézier curve and created using older version of G-LE.
June 12.
- G-LE can now model DNA of type A (and B, as before).
- The Mac OS X version now support ambient occlusion as well (albeit a bit slowly)
May 2.
- Fixed badly oriented DNA base pairs which was ruining exported DNA as PDB
- Fixed mismatch between exported base pairs and displayed base pairs
April 26.
- Fixed a bug that made cubic curves unusable on Windows.
- DNA atoms now have varying radii
- DNA sequence changed from AAAAA... to ATCGATCG... (in preparation for handling any sequence in the future)
April 5.
- A checkbox in the curve shader lets you disable the lighting, Which is cool when used together with ambient occlusion.
- When editing a DNA curve, the angle at the start of the curve now changes continuously, which is useful in the context of creating smooth animation (e.g., via interpolation in Chimera).
- The G-LE window displays the date the program was compiled. This may be useful to know which version you are using.
April 4. Fixed crash bug in surface meshing with colored selected residues.
April 3.
- It is now possible to limit the maximal length of the DNA strand, in number of base pairs. This is useful to export several strands each with a different shape but same length.
- Fixed bug in DNA to PDB export on Windows machines.
Older news.

Download and install

Compiled binaries are available for Mac OS X Lion and Windows 7. Check the download page (We will ask tiny few questions before the actual download page). The sotfware is a breathe to use with Linux distributions, but you'll have to compile it yourself (which is almost a breathe): contact us for getting access to the sources.

Who is developing Graphite - LifeExplorer?

G-LE is developped by Samuel Hornus and Damien Larivière (Fondation Fourmentin-Guilbert). It is implemented as a plugin to the Graphite research platform, which is developped by Bruno Lévy and other members of the ALICE team of INRIA. Dmitriy Sokolov developed the Molecule shader.