[456] in Software_Announce
deepview installed on Athena
daemon@ATHENA.MIT.EDU (Alex T Prengel)
Fri Mar 15 19:35:55 2002
Message-Id: <200203160035.TAA08737@dit.mit.edu>
To: software-announce@MIT.EDU
cc: alexp@MIT.EDU, cfyi@MIT.EDU, rutledge@MIT.EDU, stern@risotto,
ccummins@MIT.EDU
Date: Fri, 15 Mar 2002 19:35:39 -0500
From: Alex T Prengel <alexp@MIT.EDU>
I've installed deepview (also called Swiss-Pdb Viewer) on Athena for
Linux and SGI. Deep View is a tool for structural analysis and display
of molecular chemistry models of proteins. It can read molecular
density maps and interface to a variety of tools that generate them;
output in POV-Ray format is possible, allowing for the generation of
ray-traced images.
To run it:
add deepview
spdbv &
The SGI version often displays two copies of the main toolbar; this may be due
to an incompatibility with the default Athena Window manager (sawfish)- it
doesn't seem to happen when you use the SGI 4Dwm window manager (which
you can use by selecting the "login with Dash interface" login option).
On SGI, you will also need to set the X server to 8 bit mode- use the
login option "restart X in 8 bit mode" to select this.
tutorial samples are below /mit/deepview_v37b2/SPDBV/tutorial in the
deepview_v37b2 locker. There seems to be very little local
documentation- clicking on helpButton -> WWW Manual or Local Manual
seems to start Netscape on pages at their Web site- but they seems to
have a fair bit of online documentation there.
It will install some local configuration files below~/SPDBV the first
time you run it- these files are platform-independent.
the xv viewer on Athena can be used to view both .tga files, if "save
picture to disk" is used, and .png files, if "output to POVray 3 file"
is used as mentioned in the printing document. (Use POVray to generate
the .png image files).
We have POVray in the molden locker- to use it, once you have generated
output in a pov file (like test.pov):
add molden
povray +Itest.pov
(no space between the +I and test.pov).
spdbv outputs two files when POVray output is selected- a .pov file
and another file with auxiliary information- both should be in the
same directory when you run povray on the .pov file.
Alex
