Thank you for your interest in our work.
The following software are available for download from our web site:
IcNOE
Generate a MOLMOL macro to draw a line for every NOE in your assignment table.NoePLOT
Produce a sequential NOE plot in postscript format.
The software are released free of charge and with no warranty or assistance of any kind. If you have problem using our programs you can e-mail us a the address below.
IcNOE is a standard ANSI C++ application to generate a MOLMOL macro which draws a line for every noe assigned. MOLMOL, molecular visualization software can be obatined here. The program read an assignement table in X-plor format, and generate two file: a ".mac" file which contains the actual MOLMOL macro and a ".stat" file which contains the number of NOEs assigned,devided in intra and inter residue for every aminoacid.
Program Installation:
No particular installation is required. Just go in your home directory and umpact the tar file. Log in as superuser and link the program as follow:ln -s /install_dir/icnoe /usr/bin/icnoe
A file ".icnoe" will be created in your home directory. This file contains the color codes, average noe distances and the definitions for the stereospecific assignment for each aminoacid. It can be edited for non standard aminoacid definitions. Please be sure that the average noe distances for strong, medium and weak noes correspond to your assignment distances. Also be sure that the $HOME environment variable point to your home path.
Running the Program:
The noe table file must contains the protein sequence commented on the first line of the file in one letter code:!AGRTIMLILIV
!dHA-HN(i,i+1)
assign (residue 3 and name HN) (residue 2 and name HA#) 2.5 .6 1.5 !m
assign (residue 4 and name HN) (residue 3 and name HA) 2.5 .6 1.5 !m
assign (residue 6 and name HN) (residue 5 and name HA) 2.5 .6 2.5 !s
assign (residue 9 and name HN) (residue 8 and name HA) 2.5 .6 1.5 !m
assign (residue 10 and name HN) (residue 9 and name HA) 2.5 .6 1.5 !m
assign (residue 11 and name HN) (residue 10 and name HA) 2.5 .6 2.5 !w
assign (residue 13 and name HN) (residue 12 and name HA) 2.5 .6 2.5 !w
The program is executed at the shell prompt as follow:
icnoe <lower residue> <higher residue> noe_file.tbl
Where "lower" and "higher residue" represent the aminoacid range for which the noes visulalization is desired. The output files will be named "noe_file.tbl.mac" and "noe_file.tbl.stat".
Lines of different color intensity are drawn depending of the noe strenght. The noes intensities are determined as follow: strong noe: ~2.5A, medium noe: ~3.0A, weak noe: ~4.0A.Depending on you MOLMOL setting you might need to disable the atom name translation:
PathNames '' '' '' '' '0' '' '/usr/local/molmol/setup/pdb.lib' '' ''
Download:
IcNOE compiled for Linux (RH7.2) (last update 07/08/2002): icnoe.tar
Troubleshooting:
* At the end of each run check the macro file for the presence of lines starting with "ERR". If this lines occur, the atom definition in the assignment table is not in agreement with the "atomdef" file.* "core dumpt" at program execution:
check for the presence of the sequence as a first line in the assignment table file.* MOLMOL says: "exactly 2 atoms must be selected":
Check your noe table for non standard atoms name (example: HB1, HB2 instead of HB2, HB3!)
Bugs and Comments: Alessandro Mascioni (masci002@tc.umn.edu)
Citation:
Citation and Acknowledgements are very wellcome. If you publish papers that made use of our programs please reference them as:
IcNOE
A. Mascioni and G. Veglia,
University of Minnesota, Minneapolis
www.chem.umn.edu/groups/veglia
Noeplot is a standard ANSI C++ application to generate plot of sequencial NOEs in postscript format. The program reads an assignment table in X-Plor format. At the present stage the program plot: dHNHN(i,i+1), dHNHN(i,i+2), dHAHN(i,i+1), dHAHN(i,i+2), dHAHN(i,i+3), dHAHN(i,i+4), dHBHN(i,i+1).
Program Installation:
No particular installation is required. Just download the binary in an
installation directory, log in as superuser and link the program as
follow:ln -s /install_dir/noeplot /usr/bin/noeplot
The C++ source is available below for compilation on different systems.
Running the Program:
The noe table file must contains the protein sequence commented on the first line of the file in one letter code:!AGRTIMLILIV
!dHA-HN(i,i+1)
assign (residue 3 and name HN) (residue 2 and name HA#) 2.5 .6 1.5 !m
assign (residue 4 and name HN) (residue 3 and name HA) 2.5 .6 1.5 !m
assign (residue 6 and name HN) (residue 5 and name HA) 2.5 .6 2.5 !s
assign (residue 9 and name HN) (residue 8 and name HA) 2.5 .6 1.5 !m
assign (residue 10 and name HN) (residue 9 and name HA) 2.5 .6 1.5 !m
assign (residue 11 and name HN) (residue 10 and name HA) 2.5 .6 2.5 !w
assign (residue 13 and name HN) (residue 12 and name HA) 2.5 .6 2.5 !w
The program is executed at the shell prompt as follow:
noeplot strong medium weak noe_file.tbl
Where "strong medium weak" are the average noe intensities in your assignment table. The output files will be named "noe_file.tbl.ps".
Download:
Noeplot compiled for Linux (RH7.2) (last update 07/08/2002): noeplot
Noeplot c++ source (last update 07/08/2002): source.cppBugs and Comments: Alessandro Mascioni (masci002@tc.umn.edu)
Citation:
Citation and Acknowledgements are very welcome. If you publish papers that made use of our programs please reference them as:NoePLOT
A. Mascioni and G. Veglia,
University of Minnesota, Minneapolis
www.chem.umn.edu/groups/veglia
