Hi Ignacio,
Thanks for your detailed questions regarding recipes #4 in our 2008 3DNA
Nature Protocols paper. I am glad to know that you can reproduce recipes #1-3 and 5 without any problem. Check "
What's New" item dated 2012-04-25 for switching from Perl to Ruby as the scripting language in 3DNA v2.1.
As mentioned at the very top of "
script_h1x_h3y" for recipe #4:
# This script is a bit long, but it is actually quite simple.
# Try to understand exactly how it works, you would qualify as
# an expert 3DNA user!
Recipe #4
should be reproducible as the other ones. The best way to understand the procedures is to duplicate the whole directory to a new location, repeat and check each step as you move along.
How should I open the .r3d file to edit it? Is there a particular command or with a text editor like vi should be enough?
The .r3d file is in plain text, so you can view or edit it any way you like, e.g., using vi/emacs. Check
Raster3D homepage for details about the .r3d format.
Is this blocview.r3d file the t.r3d file that I should've obtained?
The new Ruby version of '
blocview' generates the file '
blocview.r3d' instead of '
t.r3d'. The final composite .r3d file is named '
1egk_ok.r3d', which can be loaded directly into PyMOL. Note that the original Perl scripts are still available under
$X3DNA/perl_scripts/.
All the scripts are distributed with 3DNA; reading through/between the lines is the most effective way to fully understand what's going on.
HTH,
Xiang-Jun