Nuclic acid modelling including xeno-nucleotide is a tool made to make the process of building and refiment of heavly modifed neclic acids stctures into strucule maps.
The code have been tested on the following operation systems: Ubuntu 22.04.3 LTS python 3.10.2 numpy 2.1.1 perl 5.34.0 Windows 11 26200.8037 pyhton 3.14.3 numpy 2.4.4
Download the code from github or clone the git repository into the wanted location.
git clone https://github.com/esa-lab/NAMiX.gitAfter this add the NAMIX folder to your PATH Adding NAMIX to PATH is need as the code is intened to operrate in the folder with the data so it need to be assasiable from any directory/folder.
Add the follwing to your .bashrc file or the equilant for other shells.
export PATH="path_to_namix_folder:$PATH""Edit the system enveriment variables" to add the NAMIX folder to PATH
If you want to use ROAD style blueprints for the generation of base paring restraints. you need to have perl install in addtion to python, as the code for convereting the blueprint to dot-barcket format, is taken from the ROAD repository.
NAMIX only works on the legacy .PDB file format not the new .cif
To use NAMIX, data does not need to bee located in the namix folder. Your working dirctory in the terminal neeed to be the data folder.
NAMIX can be called by just writting the following:
namix -f [filename] [options]use the following to get the following list of options.
namix -hThe -f [filename] is the only part that is mandatory
For a list of options see below
-r [file]: .pb from chimira to gennerete basepair restrains for use in phenix with .eff file.
-b [file]: make file for restrints based on ROAD blueprint for use in phenix with .eff file.
-p [prefix]: for giving files prefixes and folder suffix
-o: for overwrite folder content with same name.
-v: return mod nuc stucture to RNA.
-m: Make NAMiX output only the modded pdb file and restrint if given.\
Mods are in the format "-[base to replace see below] [modifcation_3_lettercode,resid,resid....]"
if no res ID is given all bases of the type will be replaced
-a [modifcaiton,resids]: set modifcation for adenine
-c [modifcaiton,resids]: set modifcation for cytosine
-g [modifcaiton,resids]: set modifcation for guanine
-u [modifcaiton,resids]: set modifcation for uracil
-t [modifcaiton,resids]: set modifcation for thymine
- Create a new branch:
git checkout -b feature-name. - Make your changes.
- Push your branch:
git push origin feature-name. - Create a pull request.
This project is licensed under the GPL-3.0 license.