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PostPosted: Tue Oct 13, 2009 2:32 am 
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Joined: Sat Oct 10, 2009 9:24 pm
Posts: 1

I am totally new in this field. I managed to install AutoDockTools-1.5.4 but could not have it work. I tried to follow the instruction given in README but could not make it work.

What I did was trying to copy the example commands as provided in ** SETTING UP YOUR ENVIRONMENT FOR COMMAND LINE USAGE, et al. and run in the terminal but always got error messages such as

bash: syntax error near unexpected token `('
jun@jun-desktop:~$ .cshrc - set path = /home/jun/MGLTools-1.5.4/bin $path
bash: .cshrc: command not found
jun@jun-desktop:~$ .cshrc-set path = (/home/jun/MGLTools-1.5.4/bin $path)
bash: syntax error near unexpected token `('
jun@jun-desktop:~$ .cshrc-set path=(/home/jun/MGLTools-1.5.4/bin $path)
bash: syntax error near unexpected token `('
jun@jun-desktop:~$ .bashrc - export PATH="/home/jun/MGLTools-1.5.4/bin:"$PATH
bash: .bashrc: command not found

Could anyone help me with this? Thanks a lot in advance.

MGLTools version 1.5.4 - BINARY DISTRIBUTION
Thank you for installing MGLTools version 1.5.4.
MGLTools is a collection of Python-based software tools developed
at the Molecular Graphics Lab (MGL) of the Scripps Research Institute.
This distribution contains a pre-compiled Python interpreter (version 2.5),
and the following stand-alone applications:

PMV - Python Molecular Viewer
VISION - Visual Programming Environment
ADT - AutoDockTools

To be able to start any of these applications in a Terminal Window
you will need to:
- either add "/home/jun/MGLTools-1.5.4/share/bin" to the path environment
variable in your .cshrc or .bashrc as in the following example:
.cshrc - set path = (/home/jun/MGLTools-1.5.4/bin $path)
.bashrc - export PATH="/home/jun/MGLTools-1.5.4/bin:"$PATH
- or create aliases in your .cshrc or .bashrc as in the next examples:
alias pmv /home/jun/MGLTools-1.5.4/bin/pmv
alias adt /home/jun/MGLTools-1.5.4/bin/adt
alias vision /home/jun/MGLTools-1.5.4/bin/vision
alias pythonsh /home/jun/MGLTools-1.5.4/bin/pythonsh
alias pmv='/home/jun/MGLTools-1.5.4/bin/pmv'
alias adt='/home/jun/MGLTools-1.5.4/bin/adt'
alias vision='/home/jun/MGLTools-1.5.4/bin/vision'
alias pythonsh='/home/jun/MGLTools-1.5.4/bin/pythonsh'

Rehash your path, if needed, for these changes to be in effect:
> rehash
> hash

To use PMV, ADT or VISION type pmv, adt or vision respectively;
for example:
> pmv

A Python Molecule Viewer should come up. You can load files from the
/home/jun/MGLTools-1.5.4/Data directory and start playing with PMV.
Simple networks and data for VISION are located in

To run Python interpreter type "pythonsh":
> pythonsh

** Pmv script command line options

"pmv" script can be used with the following options:

-h or --help : print help message
-a or --again : play back lastlog file
--overwriteLog : overwrite log file
--uniqueLog : create a log file with a unique name
--noLog : turn off logging
--die : do not start GUI event loop
--customizer file : run the user specified file
--lib packageName : add a libraries of commands
-d or --dmode modes : specify a display mode
modes can be any a combination of display mode
'cpk' : cpk
'lines': lines
'ss' : secondary structure ribbon
'sb' : sticks and balls
'ms' : molecular surface
'ca' : C-alpha trace
'bt' : backbone trace
'sp' : CA-spline
'sssb' : secondary structure for proteins,
sticks and balls for other residues with bonds
lines for other residues without bonds

-c or --cmode modes : specify a dispaly mode
color scheme:
'ca' : color by atom
'cr' : color by residue (RASMOL scheme)
'cc' : color by chain
'cm' : color by molecule
'cdg': color using David Goodsell's scheme
'cs' : color residues using Shapely scheme
'css': color by secondary structure element
'-i', '--interactive' : PMV interactive shell

--opt : run Python in optimized mode

Display protein as ribbon, non protein as sticks and balls
and color by atom type
pmv -i --dmode sssb --cmode cr myprot.pdb
pmv -i -m sssb -c cr myprot.pdb

Whether you plan to use this software for Commercial or Non-commercial purposes,
we ask that you acknowledge using these tools in any publications arising
from their use. Under the PMV Help menu there is a citation command providing various
papers to be cited for various tools included in this distribution.

PMV Help->citations

more license information is available below

You can refer to the license information available for the following packages:

-Python packages developed at MGL(Pmv, DejaVu, ViewerFramework,
AutoDockTools, MolKit, NetworkEditor, Vision, PyBabel, mglutil):

-Platform dependent packages:
mslib - library to compute molecular surfaces:
./LICENSES or ... cense.html
stride - the knowledge-based protein secondary structure assignment
from atomic coordinates library:
./LICENSES or ... cense.html.

Unless otherwise stated, packages that do not specify a license are released
under the MOZILLA Open Source License.

Documentation, tutorials and more information are
available online:

Several mailing lists are available for asking questions and getting answers
You can subscribe or search the archives of these lists at:

The following lists are relevant to this distribution

-autodock: a community of AutoDock, AutoGrid and AutoDockTools (ADT) users
with lots of experience to share

-pmv for questions regarding the use of PMV;

-vision for questions regarding the use of VISION;

-MGLTools support for questions regarding installing the MGLTools.

Please visit our Frequently Asked Questions page if you have any problems
installing or running our tools (
For other inquiries, send an email to mgltools:

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Translated by MaĆ«l Soucaze © 2009