Subject: Re: [modeller_usage] Tutorial for beginners?
From: Modeller Caretaker <>
Date: Mon, 05 Sep 2005 10:12:16 -0700
Cc: Modeller <>
Antonio Arroyo Luque wrote:
I try to lunch and run Modeller8v1 without any success. I use either
the Windows or the Mac version of the program. The problem I have is
that I don't know anything about Informatics but I want to learn. The
tutorial of Modeller I've found assumes certain knowledge of
Informatics. For instance, how do I launch Modeller? From the prompt
of a OS terminal?
There are many other resources available for learning informatics, and
it's really outside the scope of the Modeller tutorial to rehash them.
There is a step-by-step guide to installing and using Modeller itself in
the release notes at http://salilab.org/modeller/release.html
You will also find running instructions in the manual at
http://salilab.org/modeller/manual/node15.html
To summarise these notes: for Windows, the installer adds a "Modeller"
shortcut to your Start Menu, which opens a terminal for you. For Mac,
you need to open the Terminal application. Then you just type 'mod8v1'
and the name of your input file to run Modeller.
How to say to the program where my files are located?
As with any other program, the files are in the directory which you run
'mod8v1' in, unless you give a full path name. See step 2 at that page
in the manual I mentioned above.
For PDB files, you may have them in a different directory, in which case
it's useful to set the env.io.atom_files_directory variable. See the
example in the manual.
Is there any basic, basic, basic (something like Modeller for Dummys
- as I am) tutorial to start with? I will very appreciate your help.
I'm really not sure how the manual example could be any more
straightforward, so if there are still points that aren't clear, feel
free to follow up with me directly.
Also, any Spanish people working with Modeller?
If anybody wants to add Spanish pages (in fact, pages in any language)
for other Modeller users, there is a user-editable wiki available at
http://salilab.org/modeller/wiki/