The Superimpose Proteins plugin overlays two or more proteins in 3D space for visual comparison and calculates Root Mean Square Deviation (RMSD) values as a numeric metric on structural similarity.
Protein overlay is done either by using backbone (alpha-carbons) or by using all heavy protein atoms; and the alignment can be done on the full protein or limited to a chain.
A Fixed Reference structure is chosen, and Moving Structures are translocated to be superimposed upon the Fixed Reference. RMSD values are reported between the Fixed Reference and each Moving Structure.
For in-depth instructions, please see our docs
To run Superimpose in a Docker container:
$ cd docker
$ ./build.sh
$ ./deploy.sh [run_args]These args are passed to deploy.sh, and then forwarded to the Plugin's run.py command
usage: run.py [-h] [-a HOST] [-p PORT] [-k KEY] [-n NAME] [-v] [--write-log-file WRITE_LOG_FILE]
[--remote-logging REMOTE_LOGGING] [-r] [-i IGNORE]
Starts a Nanome Plugin.
optional arguments:
-h, --help show this help message and exit
-a HOST, --host HOST connects to NTS at the specified IP address
-p PORT, --port PORT connects to NTS at the specified port
-k KEY, --keyfile KEY
Specifies a key file or key string to use to connect to NTS
-n NAME, --name NAME Name to display for this plugin in Nanome
-v, --verbose enable verbose mode, to display Logs.debug
--write-log-file WRITE_LOG_FILE
Enable or disable writing logs to .log file
--remote-logging REMOTE_LOGGING
Toggle whether or not logs should be forwarded to NTS.
-r, --auto-reload Restart plugin automatically if a .py or .json file in current directory changes
-i IGNORE, --ignore IGNORE
To use with auto-reload. All paths matching this pattern will be ignored, use commas to specify
several. Supports */?/[seq]/[!seq]MIT