Dear fellows,
I have a protein sequence which has no template, so by using Quark I selected the first model (.pdb). I want to use modeller to mutate a amino acid at specific position and do its energy minimzation. I found a script on modeller website which has a potential to solve my query ([https://salilab.org/modeller/wiki/Mutate%20model]).
I created a folder which contain 2 files mutate_model.py (contains script present in above link) and model1.pdb (from Quark). I try to run it on terminal (suse linux platform) but unable to run this.
Do I used the correct approach regarding my query. What changes should I made in .py file and what is the script to make it executable. (version of modeller: mod9.18). Example: python mutate_model.py 1t29 1699 LEU A > 1t29.log (This source of this script is from Modeller wiki) Following error were generated when I try to used the above command on SUSE linux:
python mutate_model.py model1.pdb 100 ILE A>logfile
Traceback (most recent call last):
File "mutate_model.py", line 4, in <module>
from modeller import *
ImportError: No module named modeller
Another scripting:
mod9.18 mutate_model.py model1.pdb 100 ILE A>logfile
Traceback (most recent call last):
File "mutate_model.py", line 2, in ?
import os
ImportError: No module named os
I think it is good to copy and paste command you made and error messages you got.
I have updated it...
It's not an error message related to modeller. It's more general pyton error. Did you installed multiple python distribution? Or unknown things happened. anyway your python seems to be broken. Uninstall python and reinstall it or using Anaconda ( https://www.anaconda.com/ ) may work. (Btw, I recommend you to google with error messages before using some Q&A platform that you need not to wait several hours.)
EDIT
Sorry It is possible but I may have said wrong things. You are using SUSE Linux, which I have not used before so what I said above might be completely wrong.
Then did you check Known issues and questions with 9.19 (I know your version is 9.18 but might be related)?
https://salilab.org/modeller/9.19/release.html#issues
& I don't have any additional advise except for it (or google with "modeller" + "PYTHONPATH" https://salilab.org/modeller/manual/node14.html ). Sorry for bothering.