This is a guide intended to help you install and manage the Bio-Prodict 3DM PyMol Plugin. PyMol includes an easy-to-use plugin repository that lets you effortlessly download and install the Bio-Prodict 3DM PyMol Plugin. The latest stable version number can be found here.
You need PyMol to run this plugin. We support the 1.8.x and the 2.3.x version of PyMol at this time.
Download the PyMol binaries from PyMol.org, or get the source from SourceForge.net and build the program yourself.
This is the documentation for installation under PyMol 1.8. You may find the installation instructions for 2.x.x here.
Before you start the installation, you will need to determine which version of the plugin you would like:
The 3DM plugin is released in these two versions. If you want to use the newest features, it is recommended that you pick the Edge repository. If you would rather have the best tested version, you can pick the Stable repository.
Repository URLs:
To start the installation, you need to:
Once you have restarted PyMol, the 3DM plugin can be called from the Plugins menu.
If you encounter any problems during this installation, please proceed to the manual installation steps.
Before installing, you will need to download plugin .zip file from our servers.
Store it in a location where you can later find it again.
To start the installation, you need to:
Once you have restarted PyMol, the 3DM plugin can be called from the Plugins menu.
To find out which version of the plugin you are currently running, perform the following steps:
To update the plugin, follow these steps.
To remove the plugin, follow these steps.
For maximum compatibility, please ensure that you only have one version of the plugin installed. You can have more than one repository in your repository list in the plugin manager, but using both the edge and the stable version is not supported.
If you are running a 3DM installation on a server that is not hosted by Bio-Prodict, you will need to change the configuration of the plugin to speak to that server. To do so, you will need to alter the plugin configuration file the PyMol plugin loads. There are two ways of doing this.
Note: please contact your systems provider in order to get the correct URLs for your configuration before starting either procedure.
Currently, this procedure will need to be run every time the plugin is updated, as the default configuration is included as part of the plugin. It is, however, rather simple to perform.
If you have entered a wrong URL, PyMol will alert you of that fact when you start using the 3DM plugin.
This method will only need to be applied once, but is more involved. You may need experience with the command line for your operating system.
If you have entered a wrong URL, PyMol will alert you of that fact when you start using the 3DM plugin.
Using the PyMol plugin with your proxy is easier then ever with our integrated proxy settings screen. You can find this settings screen under 3DM > Info > Set proxy information. You do not need to be logged in to set your proxy settings. Simply enter your HTTP(S) proxy urls in the text fields, click Test proxy to verify your proxy works, and click Apply proxy settings to apply the changes. You may need to restart PyMol for the settings to take effect. If our plugin detects that access to the proxy information is required, it will automatically show the proxy information window.
If you have proxy settings defined as environment variables, these will take precedence over the those set in the built-in menu.
I entered the correct proxy server, but testing results in an error with code 407.
Your proxy requires authentication information to proceed. You may need to retrieve this information from your IT department. Please enter the proxy information in the following format:
http://<username>:<password>@<proxy_server>/ https://<username>:<password>@<proxy_server>/
I am required to connect to a proxy, but the proxy settings screen does not pop up/is empty.
Automatic update checking is turned off and our plugin cannot detect the need for a proxy. Please turn on automatic update checking in the configuration file, or enter the proxy information in the .PROXIES file. (see below)
I get OpenSSL errors when I attempt to connect using a proxy.
Your workplace may use a custom certificate to authenticate HTTPS requests. You can disable HTTPS verification from the Proxy information menu (second button on the left). This will set the verify_https option in the config file to False. You must restart PyMol for the settings to take effect. You may reenable verification in the same way.
I encounter a ConnectionError, or a message stating the my proxy is not setup correctly.
I would like to automatically transfer the proxy information.
The plugin gathers its proxy information from the .PROXIES file, situated in the directory where PyMol is run from. It will be automatically created when you click "Apply proxy settings." You can transfer this file between computers and between versions, or create it yourself. It is formatted like this (username and password optional):
{
"http": "http://<username>:<password>@<proxy_server>/",
"https": "https://<username>:<password>@<proxy_server>/"
}
I encounter an SSLError without using a proxy.
To guarantee a secure connection to the Bio-Prodict servers, we use HTTPS to establish secure connections when retrieving content. If your OpenSSL version is not up to date, you will get the following error when you try to log in:
requests.exceptions.SSLError: [Errno 1] _ssl.c:504: error:0D0890A1:asn1 encoding routines:ASN1_verify:unknown message digest algorithm
Installing the latest version of OpenSSL is easy if you currently have Homebrew installed. If not, please refer to the installation instructions on the Homebrew website.
I encounter an XQuartz error
XQuartz is a compatibility layer for OSX/MacOS that is required to launch the 3DM plugin. Please install XQuarts using the instructions on their website: https://www.xquartz.org/