On 5/28/20 6:03 PM, Xiao Ran Luo via modeller_usage wrote: > I just downloaded version 9.24 of Modeller onto by macOS version 10.14.1 > using Homebrew, but when I try to run the first few lines of the basic > tutorial, I get a lot of "command not found": > > Luos-Air:~ luoxiaoran$ >P1;TvLDH

This is an alignment file. You're supposed to save this (using a text editor) not "run" it at the terminal. I suggest you find and work through a tutorial on using the terminal before you proceed.

> Then when I try to do this (I am not sure what it is supposed to do, but > have been guaranteed that it works) I get: > > Luos-Air:~ luoxiaoran$ cd /users/luoxiaoran/Documents/modAb101

This will change your current working directory.

> Luos-Air:modAb101 luoxiaoran$ python3 modelAb101.py > > Traceback (most recent call last): > > File "modelAb101.py", line 2, in <module> > > from modeller import *# Load standard Modeller classes > > ModuleNotFoundError: No module named 'modeller'

Either something is broken in your Homebrew installation, or you have a mismatch between the Homebrew Python and Apple's Python. Reading the rest of your email though, it sounds like you may have seriously damaged your operating system (you should not be deleting the Python framework). You should probably reinstall the OS before you proceed.

Ben Webb, Modeller Caretaker

On 5/28/20 10:58 PM, Xiao Ran Luo wrote: > is there a way to prevent the mismatch between > the Homebrew Python and Apple's Python?

The Homebrew Modeller package is designed to work with Homebrew's Python, i.e. /usr/local/bin/python3 (it will also work with Homebrew's python@3.8 package, but by default that's not in your path). So if "import modeller" fails there are are really only 3 possibilities:

1. You are not using Homebrew's Python, i.e. "which python3" does not print "/usr/local/bin/python3" or "/usr/local/opt/python@3.8/bin/python3".

2. Something is broken in your Homebrew installation, i.e. "brew doctor" does not print "Your system is ready to brew."

3. Something is broken elsewhere in your operating system because of you deleting the Python framework and/or installing multiple versions of Python.

Ben Webb, Modeller Caretaker

Sorry, I just realized there are a few more things my friend recommended I install, are these all okay to install? brew install gcc brew install Caskroom/cask/xquartz brew install tcl-tk brew install python

brew tap salilab/salilab

brew install modeller

On Fri, May 29, 2020 at 12:03 PM Xiao Ran Luo xrluo00@berkeley.edu wrote:

> Thank you! I reinstalled my OS yesterday -does that mean that whatever I > broke in my operating system is fixed now? I just installed Homebrew > (technically for the first time, since my Mac reverted to an April backup) > and typed "brew doctor" and "which python3", which gave: > > > Luos-Air:~ luoxiaoran$ brew doctor > > *Please note that these warnings are just used to help the Homebrew > maintainers* > > *with debugging if you file an issue. If everything you use Homebrew for > is* > > *working fine: please don't worry or file an issue; just ignore this. > Thanks!* > > > Warning: "config" scripts exist outside your system or Homebrew > directories. > > `./configure` scripts often look for *-config scripts to determine if > > software packages are installed, and which additional flags to use when > > compiling and linking. > > > Having additional scripts in your path can confuse software installed via > > Homebrew if the config script overrides a system or Homebrew-provided > > script of the same name. We found the following "config" scripts: > > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3-config > > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3.8-config > > Luos-Air:~ luoxiaoran$ which python3 > > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3 > > Luos-Air:~ luoxiaoran$ > > > So I guess I am still not using Homebrew's Python -how do I switch to > using Homebrew's Python? And what is broken in my Homebrew installation? I > don't remember installing multiple versions of Python before April, but it > is a possibility -how do I uninstall those versions if it is needed to > switch to using Homebrew's Python? Thanks! > > > Best, > > Luna > > On Fri, May 29, 2020 at 9:53 AM Modeller Caretaker < > modeller-care@salilab.org> wrote: > >> On 5/28/20 10:58 PM, Xiao Ran Luo wrote: >> > is there a way to prevent the mismatch between >> > the Homebrew Python and Apple's Python? >> >> The Homebrew Modeller package is designed to work with Homebrew's >> Python, i.e. /usr/local/bin/python3 (it will also work with Homebrew's >> python@3.8 package, but by default that's not in your path). So if >> "import modeller" fails there are are really only 3 possibilities: >> >> 1. You are not using Homebrew's Python, i.e. "which python3" does not >> print "/usr/local/bin/python3" >> or "/usr/local/opt/python@3.8/bin/python3". >> >> 2. Something is broken in your Homebrew installation, i.e. "brew doctor" >> does not print "Your system is ready to brew." >> >> 3. Something is broken elsewhere in your operating system because of you >> deleting the Python framework and/or installing multiple versions of >> Python. >> >> Ben Webb, Modeller Caretaker >> -- >> modeller-care@salilab.org https://salilab.org/modeller/ >> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >> >

Hmm I ran /usr/local/bin/python3 and Terminal seems to be expecting something from me (the normal commands like "which python3" don't work anymore)? Sorry, I tried to find a Terminal tutorial but haven't found one that's helpful but not too difficult yet...How do I return to the normal Luos-Air:~ luoxiaoran$ and how do I edit my profile and remove that file from my PATH without deleting the python framework again?

Luos-Air:~ luoxiaoran$ /usr/local/bin/python3

Python 3.8.1 (v3.8.1:1b293b6006, Dec 18 2019, 14:08:53)

[Clang 6.0 (clang-600.0.57)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> help

Type help() for interactive help, or help(object) for help about object.

>>> which python3

File "<stdin>", line 1

which python3

^

SyntaxError: invalid syntax

>>>

On Fri, May 29, 2020 at 12:52 PM Modeller Caretaker < modeller-care@salilab.org> wrote:

> On 5/29/20 12:03 PM, Xiao Ran Luo wrote: > > Luos-Air:~ luoxiaoran$ which python3 > > > > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3 > > This is not Apple Python (/usr/bin/python3) or Homebrew Python > (/usr/local/bin/python3). Looks like you have a third version of Python > installed. > > > So I guess I am still not using Homebrew's Python -how do I switch to > > using Homebrew's Python? > > Run /usr/local/bin/python3 explicitly rather than just "python3". Or > edit your profile (maybe ~/.bashrc or ~/.zshrc) and remove > /Library/Frameworks/Python.framework/Versions/3.8/bin from your PATH. > > > Sorry, I just realized there are a few more things my friend > > recommended I install, are these all okay to install? > > You an install whatever Homebrew packages you like; they won't affect > your Modeller installation. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >

Hi Ajasja and Ben,

Thanks for the tutorial recommendation! I was hesitant to install modeller because the python problem had not been fixed yet, but am doing it now. However, when I tried to install the Homebrew version of Python using "brew install python", I got an error:

Error: The `brew link` step did not complete successfully

The formula built, but is not symlinked into /usr/local

Could not symlink bin/2to3

Target /usr/local/bin/2to3

already exists. You may want to remove it:

rm '/usr/local/bin/2to3'

To force the link and overwrite all conflicting files:

brew link --overwrite python

To list all files that would be deleted:

brew link --overwrite --dry-run python

Possible conflicting files are:

/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/3.8/bin/2to3

/usr/local/bin/idle3 -> /Library/Frameworks/Python.framework/Versions/3.8/bin/idle3

/usr/local/bin/pydoc3 -> /Library/Frameworks/Python.framework/Versions/3.8/bin/pydoc3

/usr/local/bin/python3 -> /Library/Frameworks/Python.framework/Versions/3.8/bin/python3

/usr/local/bin/python3-config -> /Library/Frameworks/Python.framework/Versions/3.8/bin/python3-config

==> */usr/local/Cellar/python/3.7.7/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python/3.7.7/bin --install-lib=/usr/local/lib/python3.7/site-packages*

==> */usr/local/Cellar/python/3.7.7/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python/3.7.7/bin --install-lib=/usr/local/lib/python3.7/site-packages*

==> */usr/local/Cellar/python/3.7.7/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python/3.7.7/bin --install-lib=/usr/local/lib/python3.7/site-packages*

==> *Caveats*

Python has been installed as

/usr/local/bin/python3

This is probably a minor error, because python appears in my brew list:

Luos-Air:~ luoxiaoran$ brew list

gcc gdbm gmp isl libmpc mpfr openssl@1.1 python readline sqlite tcl-tk xz

Luos-Air:~ luoxiaoran$

But then when I type "which python3" I still get the mystery 3rd version of python:

Luos-Air:~ luoxiaoran$ which python3

/Library/Frameworks/Python.framework/Versions/3.8/bin/python3

Luos-Air:~ luoxiaoran$

This error looks familiar, and I think troubleshooting this error was the reason I deleted the python framework in the first place (no worries, I reinstalled OS to an April backup so my Mac is not broken anymore, I think). Previously, Modeller Caretaker Ben Webb told me to: "edit your profile (maybe ~/.bashrc or ~/.zshrc) and remove /Library/Frameworks/Python.framework/Versions/3.8/bin from your PATH." which sounds like it would solve this error and all my problems, but I am not sure how to do so? Thanks!

Best,

Luna

On Fri, May 29, 2020 at 1:09 PM Ajasja Ljubetič ajasja.ljubetic@gmail.com wrote:

> Hi Xiao, > > This is a really basic question and I really recommend a good tutorial. > Maybe this one > https://www.knowledgehut.com/blog/programming/run-python-scripts? > > But in short, when you ran /usr/local/bin/python3 you entered the > interactive python environment. Only python commands will now work. > You can exit by pressing Ctrl-Z or by typing exit(). > Type *import modeller* to is if the package is installed. > > Best, > Ajasja > > > On Fri, 29 May 2020 at 13:02, Xiao Ran Luo via modeller_usage < > modeller_usage@salilab.org> wrote: > >> Hmm I ran /usr/local/bin/python3 and Terminal seems to be expecting >> something from me (the normal commands like "which python3" don't work >> anymore)? Sorry, I tried to find a Terminal tutorial but haven't found one >> that's helpful but not too difficult yet...How do I return to the >> normal Luos-Air:~ luoxiaoran$ and how do I edit my profile and remove that >> file from my PATH without deleting the python framework again? >> >> Luos-Air:~ luoxiaoran$ /usr/local/bin/python3 >> >> Python 3.8.1 (v3.8.1:1b293b6006, Dec 18 2019, 14:08:53) >> >> [Clang 6.0 (clang-600.0.57)] on darwin >> >> Type "help", "copyright", "credits" or "license" for more information. >> >> >>> help >> >> Type help() for interactive help, or help(object) for help about object. >> >> >>> which python3 >> >> File "<stdin>", line 1 >> >> which python3 >> >> ^ >> >> SyntaxError: invalid syntax >> >> >>> >> >> On Fri, May 29, 2020 at 12:52 PM Modeller Caretaker < >> modeller-care@salilab.org> wrote: >> >>> On 5/29/20 12:03 PM, Xiao Ran Luo wrote: >>> > Luos-Air:~ luoxiaoran$ which python3 >>> > >>> > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3 >>> >>> This is not Apple Python (/usr/bin/python3) or Homebrew Python >>> (/usr/local/bin/python3). Looks like you have a third version of Python >>> installed. >>> >>> > So I guess I am still not using Homebrew's Python -how do I switch to >>> > using Homebrew's Python? >>> >>> Run /usr/local/bin/python3 explicitly rather than just "python3". Or >>> edit your profile (maybe ~/.bashrc or ~/.zshrc) and remove >>> /Library/Frameworks/Python.framework/Versions/3.8/bin from your PATH. >>> >>> > Sorry, I just realized there are a few more things my friend >>> > recommended I install, are these all okay to install? >>> >>> You an install whatever Homebrew packages you like; they won't affect >>> your Modeller installation. >>> >>> Ben Webb, Modeller Caretaker >>> -- >>> modeller-care@salilab.org https://salilab.org/modeller/ >>> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >>> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> >