VIEWDOCK(1)

NAME

viewdock - Midas delegate for browsing DOCK output

USAGE

viewdock [-m] PDB_file

DESCRIPTION

One of the problems of dealing with DOCK output is that there is a large number of compounds to examine, and MidasPlus does not offer a simple interface for browsing through these compounds. Some compounds may be discarded immediately upon visual examination, since they obviously do not fit well; others may need to be examined further, depending on their scores.

Viewdock is a MidasPlus delegate that reads a list of compounds from a Protein Data Bank (PDB) format (format described below) file named on the command line, starts MIDAS to display the compounds, and presents a panel for examining, manipulating and annotating compound information. If a file named PDB_file.info is present, viewdock assumes that it is from a previous session and will use the additional compound information from that file. If viewdock is invoked with the -m flag, MIDAS will not be invoked; this option may be used to scan through the PDB file without having to look at all the atomic coordinates.

The PDB file that viewdock reads should be an edited version of the ``extended'' PDB file produced by DOCK. The file contains a list of compounds, each of which consists of a set of REMARK records, followed by the atomic coordinates in ATOM records, and terminated with a TER record. The first REMARK records must contain the compound name, e.g.,

REMARK RHOIFOLIN

The name of the compound, RHOIFOLIN in this example, must be present for viewdock to work properly; subsequent REMARK records are optional and have no format restrictions. The ATOM records for the compound follow the REMARK records. The output file produced by DOCK almost follows the PDB format; however, the last few fields in ATOM records are placed such that they cross PDB field boundaries. MIDAS follows the PDB format strictly and will reject the erroneous records, so the ATOM records need to be edited to remove the offending fields. Finally, the TER record ends a compound entry.

For each compound, viewdock stores its name, its residue sequence number, the optional information from REMARK records, and its discard state: one of deleted (entries which were discarded in a prior sessions), marked (entries which were discarded in the current session), or undeleted (undiscarded entries). All this information is presented in an interface panel which consists of several parts: a compound browser, a MIDAS residue-number field, an information window, a Discard/Restore button, and a menu bar.

The name of a compound, its MIDAS residue number and its discard state are shown in the compound browser; names of marked compounds are noted by surrounding them with short dashes (``- compound name (sequence) -'') whereas names of deleted compounds are surrounded with long dashes (``- compound name (sequence) -''). At most one compound may be selected, using either the mouse or up and down arrow keys. The MIDAS residue sequence number and the optional information of the selected compound is displayed below the browser in the sequence field and information window respectively.

Viewdock operates in one of three modes: examine, prune, and identify. In examine mode, when the user selects an entry in the browser, the compound is automatically displayed in MIDAS and any previously displayed compounds are undisplayed; picking in MIDAS has no effect. In prune mode, when the user picks a compound in MIDAS, the compound is discarded; selecting an entry in the browser does not affect what is displayed in MIDAS. In identify mode, when the user picks a compound in MIDAS, the compound is selected in the browser; selecting an entry in the browser does not affect what is displayed in MIDAS.

When the selected entry in the browser is undeleted, the button below the information window is labeled as Discard; clicking on the button will make the selected entry marked. When the selected entry is marked or deleted the button is labeled as Restore; clicking on the button will make the selected entry undeleted.

The menu bar items include:

Exit

Terminate viewdock. Viewdock can save compound state in a file called PDB_file.info, which may be used by future viewdock sessions. The Exit menu allows the user to choose whether compound state is saved and whether to terminate the associated MIDAS session.

List

Select which compounds are displayed in the compound browser based on their discard states.

Mode Select the operating mode.

Midas

Select what is displayed in MIDAS. Show Undeleted will show all undeleted compounds, while Show Displayed will show all compounds that appear in the browser.

Rewrite

Create a PDB file that only contains undeleted compounds. The new file is created by removing lines from the input PDB file (i.e., not DOCK's ``extended'' PDB file).

MIDAS INTERACTIONS

     Viewdock uses the following command to invoke MIDAS:
          /usr/local/midas/bin/midas -d dock
     This default behavior may be overridden by setting the
     environment variable VIEWDOCK_MIDAS to the appropriate MIDAS
     invocation command.

     Viewdock may also be invoked as a delegate from a running
     MIDAS session.  When viewdock detects that neither its
     standard input nor its standard output are files, it assumes
     that it was invoked through the MidasPlus delegate mechanism
     and acts accordingly.  So the command:
          delegate start viewdock /usr/local/midas/bin/viewdock PDB_file
     will start an instance of viewdock for PDB_file.  Multiple
     instances of viewdock may run simultaneously.

IMPLEMENTATION NOTES

Viewdock is implemented as a Python script, so the Python interpreter (with Tkinter, tk and tcl included) and libraries must be installed. Point your favorite web browser at http://www.python.org for information about obtaining the latest release of Python.

SEE ALSO

midas(1), python(1)

AUTHOR

Conrad Huang, Computer Graphics Laboratory, UCSF