wnprpc Example: histidines
Usage: histidines
[ port [ tag ] ]
Description: 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 []
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