Query Regarding Running Modeller From Mac
I installed modeller on Macbook Pro OS X Yosemite 10.10.5. But it does not work. I made the python files and transferred them to the bin folder in library. Then I opened terminal and gave the command: *python model-default.py > model-default.log* but it said permission denied. I installed python separately still it did not work. Kindly suggest how can I run modeller through Mac Book.
Whenever I type the command model-default.py it says no such file or directory found. How should I prepare this file. Even when I downloaded the example files there was no such file found.
On Sun, Jul 1, 2018 at 11:48 PM, Aparna Bahuguna < aparna.bahuguna04@gmail.com> wrote:
> I installed modeller on Macbook Pro OS X Yosemite 10.10.5. But it does not > work. I made the python files and transferred them to the bin folder in > library. Then I opened terminal and gave the command: *python > model-default.py > model-default.log* but it said permission denied. I > installed python separately still it did not work. Kindly suggest how can I > run modeller through Mac Book. > > -- > Aparna Bahuguna > c/o Prof. D. S. Rawat > Department of Chemistry > University of Delhi > New Delhi - 110007 >
Dear Aparna,
I hope you sourced all the modeller binaries after the installation of modeller. If not kindly source all the binaries (which locates under the bin directory) via placing them in .bashrc file.
you should have the below details in your ~/.bashrc file.
Here is my ~/.bashrc entries for modeller. You can use this as reference but don't forget to replace your paths in place of all necessary path details.
export PATH="/user/bin/modeller9.18/bin/mod9.18:${PATH}"
if [ -z $PYTHONPATH ] then export PYTHONPATH="/user/bin/modeller9.18/lib/x86_64-intel8/python2.5:/user/bin/modeller9.18/modlib/" else export PYTHONPATH="${PYTHONPATH}:/user/bin/modeller9.18/lib/x86_64-intel8/python2.5:/user/bin/modeller9.18/modlib/" fi
if [ -z $LD_LIBRARY_PATH ] then export LD_LIBRARY_PATH="/user/bin/modeller9.18/lib/x86_64-intel8" else export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/user/bin/modeller9.18/lib/x86_64-intel8" fi
Happy modelling
On 02-07-2018 10:24, Aparna Bahuguna wrote: > Whenever I type the command model-default.py it says no such file or > directory found. How should I prepare this file. Even when I > downloaded the example files there was no such file found. > > On Sun, Jul 1, 2018 at 11:48 PM, Aparna Bahuguna > aparna.bahuguna04@gmail.com wrote: > >> I installed modeller on Macbook Pro OS X Yosemite 10.10.5. But it >> does not work. I made the python files and transferred them to the >> bin folder in library. Then I opened terminal and gave the command: >> PYTHON MODEL-DEFAULT.PY > MODEL-DEFAULT.LOG but it said permission >> denied. I installed python separately still it did not work. Kindly >> suggest how can I run modeller through Mac Book. >> >> -- >> >> Aparna Bahuguna >> c/o Prof. D. S. Rawat >> Department of Chemistry >> University of Delhi >> New Delhi - 110007 > > -- > > Aparna Bahuguna > c/o Prof. D. S. Rawat > Department of Chemistry > University of Delhi > New Delhi - 110007 > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
On 7/2/18 1:58 AM, Mahesh VELUSAMY wrote: > I hope you sourced all the modeller binaries after the installation of > modeller. If not kindly source all the binaries (which locates under the > bin directory) via placing them in .bashrc file. > > you should have the below details in your ~/.bashrc file.
This is only necessary if you installed Modeller using the .tar.gz installer. Aparna is on a Mac, which has already installed Modeller in the default paths - no modifications to .bashrc are needed.
Ben Webb, Modeller Caretaker
On 7/1/18 11:18 AM, Aparna Bahuguna wrote: > I installed modeller on Macbook Pro OS X Yosemite 10.10.5. But it does > not work. I made the python files and transferred them to the bin folder > in library.
The /Library directory on your Mac is for system tools - you should not put your own files there or change anything in that directory. This is why you are getting a "permission denied" error. Put your Modeller scripts in a folder under your home directory or on your desktop, and then run them exactly as you have been doing.
Ben Webb, Modeller Caretaker
participants (3)
-
Aparna Bahuguna -
Mahesh VELUSAMY -
Modeller Caretaker