wnprpc Example: histidines


Usage: histidines [ port [ tag ] ]

De
scription: Interactive analysis of orientation and protonation state of
imidazole rings in HIS sidechains. The script connects to a running Wit!P
XML/RPC server and establishes a list of HIS (histidine) residues. The
display will be centered on the first residue in the list, and distance
monitor lines for ND1/NE1 to N,O,S distances up to 3.5 A wil be added. The
user may then execute the following commands:
  
    flip:     flip imidazol ring, update monitor lines
    next:     go to next HIS resdiue in the list
    previous: go to previous residue in the list
    charged:  change protonation state
    delta:      "        "         "
    epsilon:    "        "         "
    root mol: generate new residue list, using subtree specified by 'mol'
    exit:     disconnect from server and exit.

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -p PORT, --port=PORT  XML/RPC port to connect to [19001]
  -t TAG, --tag=TAG     connection tag to use []


Notes: (click here to see the script)

The 'histidines' script is an example of a script that connects to the XML/RPC server of an open Wit!P session. In the Wit!P session, the XML/RPC server may be started using the (hidden) command

Wit!P> xmlrpc open portnumber

at the Wit!P main prompt, or using the 'rpc' command line argument of the 'witnotp' command at the shell prompt:

$ witnotp rpc portnumber

where portnumber (integer) is a TCP/IP port number that is not in use by another service.

The 'histidines' script may then be started from within the Wit!P session:

Wit!P> <"|histidines"

or at the shell prompt:

$ histidines --port=portnumber

The script will use Python's Tkinter module to bring up the following GUI.



The molecular data subtree defined in the line labelled "root:" will be scanned to establish a list of HIS residues, and the display will be centered on the first HIS residue in the list, with monitor lines from ND1, NE1 atoms in the imidazole ring to N,O,S atoms in the rest of the subtree starting at "root". The currently displayed residue is indicated in the message line at the bottom of the GUI, together with its position in the list and the size of the list.

The "previous" and "next" buttons may be used to browse though the list of HIS residues. "charged", "delta", and "epsilon" will change the protonation state of the currently displayed reside, and "flip" will rotate the imidazole ring by 180° around the Χ2 angle.

The text in the line labelled "root:" may be changed to define a new root node for the browser (hit RETURN) in the text field to make the change active.

Clicking the "exit" button will terminate the script.


A.Widmer, NIBR/CPC/CSG-SB