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Download macOS High Sierra for Mac & read reviews. Increased security. This operating system lays a foundation for future upgrades. Eliminate devops. Getting Anaconda to work with Oh My ZSH on Mac OS X. There’s a block of code the anaconda installer added to the end of the file. Mine looks something like this.
- 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.
Free Download Mac Os X 10.4
To install Modeller using the 'conda' package manager, simply run froma command line
conda config --add channels salilab
conda install modeller
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
- Log on as a Computer Administrator user (usually the first user youcreate is an administrator).
- 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.
- 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'.)
- 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.
- 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.
- 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.
- 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
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):
- Download the Macinstaller to your Desktop.
- Double-click on the modeller-9.24.dmg file to open the diskimage.
- 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.
- 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.
- 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.
- 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.
- 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.rpmOn 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.
- 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.)
- 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 ~'.
- To uninstall Modeller, run the following command:'rpm -e modeller'.
If you have not used Modeller before, proceed to theGetting started section.
![Download free mac os x Download free mac os x](/uploads/1/2/4/4/124406555/602335644.png)
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.
- Download the correctDebian/Ubuntu package for your architecture.
- 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
- 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.)
- 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 ~'.
- 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.
Anaconda Mac Uninstall
- Download the generictarball (.tar.gz) file into a temporary directory on your computer.
- 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 - Go to the ./modeller-9.24 directory and run the installationscript:cd modeller-9.24
./InstallAnswer several questions as prompted. If you make a mistake, you can re-runthe script. - 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.
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.
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.
- 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). - 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. - 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:
Platform | Modeller executable type | Tested systems |
---|---|---|
Linux i686 PC (Intel Pentium, AMD Athlon etc.) | i386-intel8 or i386-absoft | Fedora 31, RH 9[1], RH Enterprise 5 & 6, Ubuntu 18.04, FreeBSD-4.11[2][3] |
Windows i686 PC (Intel Pentium, AMD Athlon etc.) | i386-w32 | Windows 7 (32-bit and 64-bit), Vista (32-bit), XP Service Pack 3 |
Windows x86_64 PC (Intel Xeon 64 etc.) | x86_64-w64 | Windows 7 (64-bit) |
Apple Mac (Universal) | mac10v4 | 10.6 (Snow Leopard), 10.11 (El Capitan) and 10.15 (Catalina) on Intel (32-bit and 64-bit) |
Opteron/Intel Xeon64 (AMD64/EM64T) | x86_64-intel8 | RH Enterprise 5, 6, 7 & 8, Fedora 31, Ubuntu 18.04 |
AIX | rs6000 | AIX V5.1 on a PowerPC p630 |
What’s OpenCV?
Ahhh, computer vision, such a cool field! Lately, I’ve been trying to become more knowledgeable about CV and image processing in python. OpenCV (CV = ‘computer vision’) is an excellent open source computer vision software library written in C++ that supports C++, C, Python, Java, and Matlab API’s. OpenCV will supply you with functions that will let you detect faces in images, track objects in a video, and perform any number of image processing tasks.
The only problem is: how the hell do I install OpenCV so that I can use it in conjunction with a Jupyter notebook? Let’s be honest, most likely you’re either you’re using a Jupyter notebook, Spyder, or the ipython terminal (if you’re a real sadist) to test your python code. And especially if you’re coding for image processing, you’re going to want to view your progress without having (a) a million separate images open and (b) having to wait for Spyder to inevitably crash. That’s the beauty of a Jupyter notebook - when you’re using it with Matplotlib, you can just display your images and videos in a living document!
For me, my ideal OpenCV situation would be for me to be able to simply type and evaluate the following
import
statements with zero errors or package conficts:Problems with traditional installation methods
There are many ways to install OpenCV. The standard approach is to download it from the OpenCV website and then compile and install OpenCV using the software building utility “CMake” all within a virutal Python environment. I’ve gone down this route according to Adrian Rosebrock’s fabulous installation walkthrough, and if you just want to have access to OpenCV 3.0, I suggest you consider it. But, at the end of the day, there are even more steps required after Adrian’s 9 steps to get OpenCV compatible with a Jupyter notebook. Other installation walkthroughs I’ve found tend to be generally convoluted and assume that you have Homebrew, XCode, maybe MacPorts, or just experience in general with installing and building software packages. Wouldn’t it be great if we could just run something analogous to
pip install opencv
?If you’re like me (maybe you’re not) I often think that
pip install
‘ing a Python package is the same thing as R’s install.packages
function - while we get similar functionality, R packages come with the luxury of basically never interfering with other R package dependencies! If one package needs a newer or older version of some other package you’ve already installed, install.packages
will most likely just take care of everything for you. Python packages, on the other hand, will often have dependencies on specific versions of other packages, so if you pip install
one package, other package may fail to import because their dependent packages have been updated. That’s why we use virtual environments; my favorite method for creating and running virtual environments is with Anaconda, a Python distribution that comes with Sklearn, Scipy, NumPy, Jupyter notebook, and most of the other essential tools a data scientist needs when using Python.Overall, I installed OpenCV cleanly in just a few steps:
- Install Anaconda, make Anaconda’s Python your system’s default Python (skip if you already have this).
- Create a virtual environment.
- Make sure all Conda packages are up-to-date.
- Run
conda install -c https://conda.binstar.org/menpo opencv
- Test.
(1) Install Anaconda. (Skip if you already have Anaconda).
First off, I’m still a python 2 guy. Yeah, there’s python 3, but I grew up on Py 2.7 and it’ll take a lot to pry it from my cold, dead hands. So I have a python 2.7 Anaconda environment running on my computer. Your choice.
I went to the Anaconda downloads page and got the Python 2.7 Mac OS X 64-Bit command-line installer, so that we can install everything from Terminal.
After downloading that, navigate to your Downloads directory (if you’re new to the Terminal, just open the Terminal application and type
cd $HOME/Downloads
).While still in Terminal, enter
Awesome, now you’ve downloaded and installed Anaconda.
(1.b) Make Anaconda your default python installation.
For data science, Anaconda rules. Ideally, when you’re in Terminal and you type
python
, you’d like for the Anaconda python installation to be the default python that starts running instead of what comes installed by default on a typical Macbook. Why? Well, using Anaconda we can just import NumPy, import any Scikit Learn funciton, import Matplotlib, etc.To see what I’m talking about, type this in Terminal:
If you get
/usr/bin/python2.7
, you’re not using the Anaconda installation. To change this, you’ll need to change your bash_profile so that the default path to the python installation in the Anaconda directory. If you don’t have a .bash_profile file in your home directory, do this:This just created that file. Next, open the .bash_profile page and add this line:
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export PATH=”~/anaconda/bin:$PATH”
Finally, you have to make your system update python path the with your new settings, so in Terminal type
![Install anaconda on mac Install anaconda on mac](/uploads/1/2/4/4/124406555/788730676.png)
(2) Make an Anaconda virtual environment
Anaconda has great documentation if you ever get lost using their tools, but otherwise they’re pretty easy to use. To create a virtual python 2.7 environment called “py27,” run this:
To enter this virtual environment, we use Conda’s
source activate
function:Mac Anaconda Prompt
If the environment is running properly, you should see
(py27)
preceding the $
sign at the command prompt in Terminal. In this environment we have access to Anaconda’s python package installer, conda install
, so that we can install packages at will in this “bubble” without messing up dependencies (basically breaking python) in any other environment. Side note: if you want to exit this py27 environment, just enter source deactivate
in Terminal.(3) Update packages
Where Can I Download Mac Os X
Just to be safe, I updated all of my python packages while inside of my py27 environment. It’s ridiculously easy with Anaconda:
(4) Install OpenCV
With Anconda we can install python packages within a specific Conda environment using
conda install
instead of pip
, the typical python package management system.Anaconda Terminal Mac
Next, I would normally suggest just typing
conda install opencv
at the command prompt, but this (unsurprisingly) lead me to a package conflict with NumPy! Yep, the version of OpenCV that Conda installed relied on a specific release of the NumPy package that was actually in conflict with the one that was just updated in step (3). OK, to be honest, maybe I brought that upon myself with updating the packages the way I did. But, there’s a work around that functions with this latest update of NumPy: install OpenCV directly from the Menpo project:(5) Fire up a Jupyter notebook and test!
The Anaconda environment should now have everything we need to start analyzing images in a self-contained little Jupyter notebook. Test it out. First, launch a Jupyter notebook from the terminal:
Next, see if everything is installed correctly; hopefully you’ll be able to run this sans errors:
Install Anaconda Mac Os
If successful, you’ll be able to readily access OpenCV functions with the package prefix
cv2
!