• Anaconda Terminal Mac
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Anaconda Terminal Mac

MacOS graphical install¶. Download the graphical macOS installer for your version of Python. RECOMMENDED: Verify data integrity with SHA-256.For more information on hashes, see What about cryptographic hash verification? Double-click the downloaded file and click continue to. Operating system: Windows 8 or newer, 64-bit macOS 10.13+, or Linux, including Ubuntu, RedHat, CentOS 6+, and others. If your operating system is older than what is currently supported, you can find older versions of the Anaconda installers in our archive that might work for you. Anaconda is an open, cross-platform runtime for Anaconda for Multimedia Fusion 2, with support for Windows, Linux and Mac OS X. Mp2.dk/anaconda GPL-3.0 License.

This tutorial will help you to install Anaconda for Mac OS.

Anaconda is both a package manager, python distribution and is incredibly useful for data tasks as it comes bundled with many scientific packages including sci-kit learn, SciPy, Pandas and NumPy.

Additionally it’s the recommended method for installing Jupyter Notebooks.

Installing Anaconda

Personally I prefer to install Python via the graphical interface because it’s a friendly and easy method.

1. Firstly visit the Anaconda website where you will have the choice to install either Python 2.7 or Python 3. I would recommend downloading the Python 3x. because this will be more supported in the future.

2. After successfully downloading Anaconda, locate it within your download folder and double click on the .pkg file.

3. Click continue.

4 – You will now start the Anaconda3 installer process, click continue.

5. The installer provides a notification saying that it will update your bash profile and will install Anaconda3 within your PATH. Click continue.

6. Click continue to reveal the License Agreement.

7. Now you will need to read and click Agree for the Anaconda licensing agreement, then click continue.

7. Click on the install button.

8. You will need to enter your password which is the same as your Mac login password. Then click Install Software.

9. Click on Continue.

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10. After completing the installation simply click close. Then you can move the Anaconda installer file to the trash bin.

Anaconda Frequently Answered Questions

• Installation

What's new in version 9.24?

9.24 is primarily a bugfix release relative to the last public release(9.23). Major user-visible changes include:

• Single-chain models, which are currently assigned a blank chain ID, cannow instead be labeled 'A' by setting automodel.blank_single_chain toFalse, or by setting the same argument to alignment.append_sequence(),model.generate_topology(), or model.build_sequence(). The default forthis argument will change to False in a future Modeller release.
• Bundled version of HDF5 updated to 1.10.5.
• The MEX and ABU residue types are no longer automatically convertedto CYS, regardless of the setting of env.io.convert_modres; they aretreated as any other ligand.
• Bugfix: alignment.append() no longer fails when given a very longfile name to read.

See the Modeller manualfor a full change log.

Installation

Modeller is free for academic use. To obtain an academic license key, whichyou will need during the installation, complete thelicense agreement. The license keywill be sent to you in an email from our license server. Forcommercial or governmental use, licensing is handled byBIOVIA.

Modeller is available for Windows, Mac OS X, Linux, and some Unixvariants (see the full list of platforms).Please refer to the relevant section below for installation instructions:

For Anaconda Python ('conda')

Modeller is packaged to use with theAnaconda scientific Pythondistribution for Windows, Linux and Mac.

To install Modeller using the 'conda' package manager, simply run froma command line

conda config --add channels salilab
conda install modeller

You will be prompted after installation to edit a file to add your Modellerlicense key. Alternatively, set the KEY_MODELLER environment variableto your license key before you run 'conda install'.

For Windows

1. Log on as a Computer Administrator user (usually the first user youcreate is an administrator).
2. Download the Windowsinstaller and save it to your Desktop. The 32-bit version should work on anyWindows machine; the 64-bit version will only work on 64-bit versions ofWindows.
3. Double-click on the modeller9.24-32bit ormodeller9.24-64bit file to start theinstaller. (Windows Vista or 7 will pop up a User Account Control window at thispoint warning about an unidentified program - click 'Allow'.)
4. Tell the installer where to install Modeller, and enter your Modellerlicense key when prompted. This must be typed exactly as given in the emailyou received from our license server.
5. Once the install is complete, you can run Modeller scripts from a regularPython command line or IDLE GUI, if you install any version of Pythonbetween 2.3 and 3.8 from the Pythonwebsite. (To run a Modeller script in IDLE, right-click on it, select'edit in IDLE', then hit F5 to run it; if you install the 32-bit version ofModeller, this will only work with the 32-bit version of Python, and likewisefor the 64-bit version.)Alternatively, you can usethe Modeller link from the Start Menu to start a Command Prompt from whereyou can run Modeller scripts. It is usually not a good idea to simplydouble-click on a Modeller script to run it, as the output will disappearas soon as the script finishes.
6. Examples can be found in the 'examples' folder. You can type'run_tests' in this folder to run them all (an 'import site' warning is normal,as is a failure to load the 'socket' module for some examples). Note,however, that if you use NT/2000/XP, and are NOT an Administrator user,or you are using Windows Vista or later with UAC turned on (the default) youwill first need to make a copy of this directory elsewhere, as Windowswill not allow Modeller to write output files into this directory.
7. To uninstall Modeller, use the 'Uninstall' link on your Start Menu(again, you will need to be logged on as a Computer Administrator).

If you have not used Modeller before, proceed to theGetting started section.

Note: the Windows installer also supports silent (unattended) installation.To install silently, run the installer with the /D flag to specify installlocation and /KEY to specify the Modeller license key, e.g.modeller9.24-32bit.exe /S /KEY=xxx /D=C:Program Filesmodeller.Note that the /D option must come at the end of the command line and thepath must not be quoted.

For Mac OS X

If you are using the Homebrew package manager,you can install Modeller by simply running
brew tap salilab/salilab
brew install modeller

Alternatively, we provide a Modeller installer, which should work on both32-bit and 64-bit Intel Macs (it does not work on older PowerPC-basedMacs):

1. Download the Macinstaller to your Desktop.
2. Double-click on the modeller-9.24.dmg file to open the diskimage.
3. Double-click on the Modeller 9.24.pkg file within this image(if your Mac complains that the package is by an unidentified developer,right-click or control-click on it instead and select Open from the dropdownmenu, then Open again in the confirmation dialog).Enter your license key when prompted by the installer.

   Note: you can also use Apple's command line installerutility to install the package, but this will not fill in the license key;you would need to then manually edit the file /Library/modeller-9.24/modlib/modeller/config.py to fill in the license variable.

4. Once the install is complete, you can run Modeller scripts like any otherPython script: for example, you could run theModeller script foo.py by typing'python foo.py' from a Terminal window. Alternatively, you can type'mod9.24' to run Modeller.(See below for example scripts.) (Modeller itself can befound in the /Library/modeller-9.24/ directory.) Note that Modelleris set up to work with the standard Apple-provided Python, i.e./usr/bin/python; to make it work with other versions of Pythoninstalled on your system, you may need to modify PYTHONPATH.
5. To uninstall Modeller, run the following from a Terminal window (all onone line):'sudo rm -rf /Library/modeller-9.24/ /usr/local/bin/mod9.24/Library/Python/2.?/site-packages/modeller.pth/var/db/receipts/org.salilab.modeller.*'.

If you have not used Modeller before, proceed to theGetting started section.

For Linux (RPM)

The Linux RPM installer should install on any modern RPM-based Linuxsystem, such as RedHat Enterprise, Fedora, or SuSE. It can also beinstalled on non-RPM systems such as Gentoo. (For .deb-based systems suchas Debian or Ubuntu, we recommend the Debian/Ubuntu packageinstead.)

If you do not have root access to your Linux system, or wish to install ina non-standard location, you can use the generic Unixinstaller instead.

Prerequisites:glibc >= 2.3 (although it may work with glibc 2.2;see below); and glib >= 2.2 (installed on most Linux systems by default; can beobtained from the GTK+ websiteif your distribution doesn't have a 'glib' or 'glib2' package.) For oldoperating systems such as RedHat 8.0, seethis page in the Modellerwiki.

1. Download the correctRPM file for your architecture.(If in doubt, run 'uname -m' from a terminal on your Linux box.'i386' (or i586/i686) is for 32-bit machines such as the Pentium. x86_64 is formost 64-machines such as the Opteron or Intel Xeon64.)For the security conscious, all of thesefiles are GPG signed.
2. Install the RPM file by running the following command (either logging inas the root user, or by prepending the command with 'sudo'),replacing XXXX with the Modeller license key(and i386 with x86_64 if necessary).

   env KEY_MODELLER=XXXX rpm -Uvh modeller-9.24-1.i386.rpm

   On a built-from-source system such as Gentoo, the original 'rpm' commandshould work, although you will probably need to build the rpm package itselffirst, and append the --nodeps option to the command.

3. If you have any version of Python between2.3 and 3.8 installed on your system, you should be able to use Modellerfrom a regular 'python' interpreter.For example, you could run the Modeller scriptfoo.py by typing 'python3 foo.py' from a command line (e.g.a GNOME terminal window, KDE Konsole window, etc.). (On some systems, you mayneed to use 'python2' or 'python' instead.)Alternatively, if you don't have Python installed, you can run Modellerby typing 'mod9.24' from a command line.(See below for example scripts.)
4. Documentation and examples can be found in the/usr/lib/modeller9.24/ directory. Note that you will need to make acopy of the examples directory in order to use it, e.g.'cp -a /usr/lib/modeller9.24/examples ~'.
5. To uninstall Modeller, run the following command:'rpm -e modeller'.

If you have not used Modeller before, proceed to theGetting started section.

For Linux (Debian/Ubuntu)

The Debian/Ubuntu package should install on any modern .deb-based system.(It was, however, built and tested on an Ubuntu 14.04 (Trusty Tahr) machine,so may not work on older systems.)If you do not have root access to your Linux system, or wish to install ina non-standard location, you can use the generic Unixinstaller instead.

1. Download the correctDebian/Ubuntu package for your architecture.
2. Install the package by running the following command,replacing XXXX with the Modeller license key(and i386 with x86_64 if you are using the 64-bit installer).

   sudo env KEY_MODELLER=XXXX dpkg -i modeller_9.24-1_i386.deb

3. If you have any version of Python between2.3 and 3.8 installed on your system, you should be able to use Modellerfrom a regular 'python' interpreter.For example, you could run the Modeller scriptfoo.py by typing 'python3 foo.py' from a command line (e.g.a GNOME terminal window, KDE Konsole window, etc.). (On some systems, you mayneed to use 'python2' or 'python' instead.)Alternatively, if you don't have Python installed, you can run Modellerby typing 'mod9.24' from a command line.(See below for example scripts.)
4. Documentation and examples can be found in the/usr/lib/modeller9.24/ directory. Note that you will need to make acopy of the examples directory in order to use it, e.g.'cp -a /usr/lib/modeller9.24/examples ~'.
5. To uninstall Modeller, run the following command:'sudo apt-get remove modeller'.

For generic Unix

This installer contains binaries for Linux and AIX.If installing for Linux, the prerequisites are the same as forinstalling the RPM.

1. Download the generictarball (.tar.gz) file into a temporary directory on your computer.
2. Open a console or terminal (e.g. xterm, Konsole, GNOME terminal) andchange to the directory where you downloaded the .tar.gz file.Unpack the file with the following commands:

   gunzip modeller-9.24.tar.gz
   tar -xvf modeller-9.24.tar

3. Go to the ./modeller-9.24 directory and run the installationscript:

   cd modeller-9.24
   ./Install

   Answer several questions as prompted. If you make a mistake, you can re-runthe script.

4. You can run Modeller by using the modpy.shscript in the bin directory under the directory you installedModeller in. For example, if you installed Modeller in /opt/mod/,then if you have any version of Python between 2.3 and 3.8 installed,'/opt/mod/bin/modpy.sh python3 foo.py' will run Modeller with ascript file called foo.py (depending on your system, you may need touse python2 or python instead of python3).(If you add the Modeller libraries to your path, as detailed by theInstall script output, you can omit the modpy.sh scriptentirely and run a Modeller script with a simple 'python3 foo.py'.)If you don't have Python installed,'/opt/mod/bin/mod9.24 foo.py' will run Modeller on the same script.(See below for example scripts.)

If you have not used Modeller before, proceed to theGetting started section.

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Getting started

Once Modeller is successfully installed, please refer to thedocumentation, in particular theonline manual and theModeller tutorial for information on usingthe program and example scripts. You will also find several example scriptsin the examples directory after you install Modeller.

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Please also check periodically at thepatches page in theModeller wiki for hotfixes to the currentrelease.

Known issues and questions with 9.24

Please also check the Modeller FAQ and themailing list archives.

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1. Standard Python libraries like os aren't availableor I get warnings such as ''import site' failed' or'Could not find platform independent libraries <prefix>'
   The mod9.24 script uses a built-in copy of thePython 2.3 interpreter, but not theaccompanying modules. It is recommended not to use themod9.24 script to run Modeller for this reason; see the instructionsabove for running Modeller with Python.(Note that you only need the Python 2.3 modules if you are tryingto import non-Modeller modules; you don't need them to run regularModeller scripts, so you can often ignore these warnings).
2. Trying to load Biopython (or some other Python modules) in a Modellerscript gives errors about PyUnicodeUCS2
   The built-in Python interpreter in the mod9.24 script is compiled with4-byte Unicode support ('UCS4') on most platforms and is notcompatible with any modules compiled with 2-byte Unicode ('UCS2').This is a Pythonlimitation. To avoid this problem, don't use the mod9.24 scriptto run Modeller; see the instructions above for running Modeller with Python.
3. I get an error similar to the following when starting Modeller: 'error while loading shared libraries: libmodeller.so.5: cannot restoresegment prot after reloc: Permission denied'
   Linux builds of Modeller rely on the Intel Fortran libraries, which are notcompatible with strict SELinux policies enforced in some versions ofFedora and RedHat Linux. You can make Modeller work by enabling theallow_execmod SELinux boolean, disabling SELinux entirely, orlabeling the Modeller libraries as containing text relocations using thesemanage utility. (The last is preferable, and should have been doneautomatically for you already if using the RPM installer.)More technicaldetails (see the execmod section).

Tested platforms

MODELLER runs on Pentium PC's (Linux and Windows), Apple Macintosh (OS X),Linux x86_64 systems, and workstations from IBM (AIX). The actual platformswhich 9.24 has been tested on are shown below: