TUTORIAL OPEN3DTOOLS

(Tools developed by Dr. Paolo TOSCO and Dr. Thomas BALLE)

Tutorial made by Dr. Enrico PERSPICACE

Workstation:

_ Windows Vista Home Premium (SP2) – 32 Bit – German language

_ Processor Intel® core™2 Duo CPU T5450 at 1.66 GHz – 3 Go RAM

Download and installation of Open3DTOOLS suite:

Open3DALIGN, Open3DGRID and Open3DQSAR can be found here:

http://open3dalign.sourceforge.net/ (Open3DALIGN)

http://open3grid.sourceforge.net/ (Open3DGRID)

http://open3dqsar.sourceforge.net/ (Open3DQSAR)

Those pieces of software can be installed independently.

I will only show you how to install Open3DQSAR but it is the same for Open3DALIGN and Open3DGRID.

Please go to: http://open3dqsar.sourceforge.net/?Downloads

Select your operating system by clicking on it (for me it is Windows). You will be redirected to sourceforge.net website.

If you don’t know the version of your operating system (32 or 64 Bit), you can download “choose_version.exe” and launch it.

Then, you can download the right version (for me it is: open3dqsar-2.25_windows_sse3_setup.exe).

Open3DQSAR uses also OpenBabel for file extension conversion. You can find a version of OpenBabel on the same website (openbabel_for_open3dtools_windows_setup.exe)

Now, you can install Open3DQSAR followed by OpenBabel by clicking on it and following the instructions.

Once installed please launch Open3DQSAR

When you launch the first time Open3DQSAR, you can see:

_ the working directory automatically set to: C:\open3dtools

_ the location of OpenBabel automatically set to: C:\open3dtools\bin

But some information are missing such as path for QM engine, CS3D, GRID, GNUPLOT and PyMOL. None of those pieces of software is strictly required to run Open3DQSAR, but they may help visualization of results (GNUPLOT and PyMOL) or allow carrying out specific MIF calculations (QM engine, CS3D, GRID).

I will just show you how to set PyMOL and GNUPLOT.

Go on your desktop, right click on Computer icon and select properties.

The “system” window will open.

Click-on “Advanced system parameters”

The “System properties” window will open.

Click-on “Variables environment” and on “New”

And now I will create a new variable:

The name of the variable can be found when you launch Open3DQSAR:

So, you just have to enter the name of the variable as follow:

Followed by the path (for me it is C:\Program Files\DeLano Scientific\PyMOL\PyMOL.exe):

Then click on OK.

Your PyMOL path is now set.

You can also set the variable environment directly in Open3DQSAR by typing:

env gnuplot=”C:\Program Files\gnuplot\bin\gnuplot.exe” (for example for GNUPLOT)

Press Enter button:

Using the same procedure you can add COSMOsar3D, GRID, GAMESS, GAUSSIAN. But those pieces of software are not required for 3D-QSAR calculation using Open3DQSAR tool (Please see http://Open3DQSAR.sourceforge.net/?Description for more information).

Now your Open3DQSAR is set and we can run it using an example.

The example is located in: C:\open3dtools\Open3DQSAR\example\MM\

Open sample_input.inp file with notepad (or, even better, Notepad++).

Right click on the file, open.

Choose open with already installed program.

And choose Notepad (or Notepad ++, if you installed it).

Please be sure that Notepad is not always used to open sample_input.inp file.

Now you have just to follow the instructions as depicted into the file.

First of all, import ref_e2.sdf file

When you click on “Enter” button, molecules will be loaded and viewed in PyMOL.

Now you can follow exactly the procedure as described in sample_input.inp file.

NB: you have just to type first characters and press “TAB” button to have the commands completed. For example, if you write just “typ” and press “TAB”, “type=” will be automatically written.

Depending of the power of your computer, to save some RAM you might want to create a new variable environment as O3_SAVE_RAM (Name), and set to “YES”. This has a rather small impact on speed and allows carrying out calculations on large datasets.

For further information on different keywords please go to:

http://Open3DQSAR.sourceforge.net/?Description:Keywords

When you finished all calculations, you can visualize PLS pseudo-coefficients maps with PyMOL, MOE or MAESTRO.

I will show you an example with PyMOL.

Open PyMOL

In command line, type:

load c:\open3dtools\Open3DQSAR\example\MM\ffdsel_coefficients_fld-01_y-01.grd, steric

Set the isocontour value for positive values (this value can be modified for optimal visualization of isocontours)

isosurf steric_pos, steric, 4.0e-03

Set the isocontour value for negative values (this value can be modified for optimal visualization of isocontours)

isosurf steric_neg, steric, -4.0e-03

Set color in red for positive values

Color red, steric_pos

Set color in blue for negative values

Color blue, steric_neg

This explanation is from the blog of Paolo TOSCO and can be found:

http://sourceforge.net/mailarchive/forum.php?thread_name=3B9C0DC0-2134-449F-A9A6-5770F8A41A6D%40unito.it&forum_name=Open3DQSAR-discuss

HAVE FUN ;-)

Enrico PERSPICACE