This is a guide intended to help you install and manage the Bio-Prodict 3DM YASARA Plugin.
The recommended way to install YASARA plugin is by using the version that comes with your YASARA distribution. This ensures that the version of YASARA is compatible with the version of your plugin. You can retrieve YASARA from the YASARA downloads page. Every YASARA download comes with the 3DM plugin pre-packaged. The latest stable version number can be found here.
To verify that the plugin works correctly, please confirm that the top menu bar contains the 3DM option. If it is listed, you can verify the installation completely by Clicking on 3DM > Info > About Bio-Prodict 3DM. When a screen comes up with information about the plugin, the installation was completed successfully.
If the 3DM menu is not listed in the top menu, you may install it from inside YASARA. This can be done using the Help > Install > 3DM Plugin menu option. You must restart YASARA after the installation has finished. If the 3DM button still does not appear, please verify that Python 2.7 has been installed. It can be installed using the Help > Install > Python menu option.
If the 3DM menu is listed, but no screen shows up after clicking About Bio-Prodict 3DM, please scroll down to the bottom of the page for troubleshooting information.
If you want to update your plugin installation yourself without reinstalling YASARA, you can update the plugin yourself. Note: if your installation was mediated by the Bio-Prodict team, this is the recommended installation process.
Your YASARA installation is now updated to the latest stable version.
Using the YASARA 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 OK to apply the settings. You do not need to restart YASARA for the settings to take effect.
If you encounter an error while testing your proxy settings, contact your system administrator. After you have successfully adjusted your settings, YASARA will show a message confirming the adjustment. If your settings have remained unchanged, you will be notified as well. You can always find the currently applied proxy settings by looking at this menu. The text field headers will show the currently active proxy settings.
If you have proxy settings defined as environment variables (for example, if you previously used the old method of setting proxy information) these will take precedent over the those set in the built-in menu. Administrators can adjust the proxy adresses manually by adjusting the .PROXIES file in the 3DM plugin directory.
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 would like to automatically transfer the proxy information.
The plugin gathers its proxy information from the .PROXIES file, situated in the directory
where YASARA 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>/"
}
The procedure for working with the YASARA plugin through an HTTP proxy is the same as that for YASARA (please refer to page RYwwataHp.html in your YASARA documentation for more in-depth instructions and a background), except with HTTPS. To reiterate the procedure: It requires setting the https_proxy environment variable on your system.
In Windows, you can add it to the autoexec.bat file:
set http_proxy=http://yourproxy.yourdomain.com:3128
set https_proxy=http://yourproxy.yourdomain.com:3128
Alternatively start the control panel, search for 'env' and click 'Edit the system environment variables' (Windows 10, setting variables for your own account may be broken), or search the settings for 'environment' (Windows 8), or enter the Start menu, right-click on Computer, then click Properties > Advanced system settings > Advanced tab > Environment variables > New (Windows 7 and older), or enter the Start menu, type 'Accounts' into the search box, go to 'User Accounts' and 'Change my environment variables' in the bottom left corner (Windows 7 without admin privileges).
Having made the change, restart your computer.
In Linux, it depends on your shell, e.g. bash users can add it to the ~/.bashrc file. If you launch YASARA with a desktop shortcut, please consult the documentation of your Linux distribution how environment variables are set there.
http_proxy="http://yourproxy.yourdomain.com:3128" export http_proxy https_proxy="http://yourproxy.yourdomain.com:3128" export https_proxy
In MacOSX 10.8 and newer, environment variables must be added to the file /etc/launchd.conf, e.g. the following entry:
setenv http_proxy http://yourproxy.yourdomain.com:3128
setenv https_proxy http://yourproxy.yourdomain.com:3128
NOTE that due to a MacOSX caching problem you may have to reboot your computer after
making the change. Type 'env' in a terminal to verify it worked.
In MacOSX 10.7 and older, you can add them to the .MacOSX/environment.plist file, like in the following example:
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> <plist version="1.0"> <dict> <key>http_proxy</key> <string>http://yourusername:yourpassword@yourproxy.yourdomain.com:3128</string> <key>https_proxy</key> <string>http://yourusername:yourpassword@yourproxy.yourdomain.com:3128</string> </dict> </plist>
NOTE that due to a MacOSX caching problem you may have to reboot your computer after making the change. Type 'env' in a terminal to verify it worked.
Instructions have been copied (with small alterations) from the YASARA documentation.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 YASARA 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, YASARA 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, YASARA will alert you of that fact when you start using the 3DM plugin.
Please check that you have the correct version of Python installed. The 3DM YASARA Plugin relies on Python 2.7 being available on your system. To install the proper version of Python, please visit the Python Downloads page and download the latest version of the 2.7.xx series.
After the download has finished, start the installer. During the installation process you will be presented with a list of components. At the bottom of this list the option "Add python.exe to your PATH" is demarkated by a red cross. Click this component and select "This feature will be installed to the local hard disk" (the first option). Continue the installation as normal.
After restarting YASARA, the plugin should function as expected.