Java Based Image Display for Protein Crystallography
Java based Image Display
John W. Campbell
Introduction
This Java based image display software for Protein Crystallography is
based on earlier C/Fortran based image display software developed at
the Daresbury Laboratory in the 1980's as part of a toolkit called
XDL_VIEW.
The general features of the image display will be familiar
to users of that package. The original package is still available
through the CCP4 project.
Note that, in the Java version, new
scrollbars provide an alternative way of zooming (left scrollbar) and
moving around (right and bottom scrollbars) the image.
This is work under development and is being made available here for
trial and feedback from interested parties. Some demonstration images
are available to try out some of the features of the display. There
are also options for running an image display program with your own
images but you will need to set up permissions to enable
your own files to be accessed. This is also a requirement if you want
to use the image printing options (to file or printer) of the display
or to paste text (e.g. file names) into the program.
Documentation
Brief documentation, indicating how to use the various program
functions, is available via the 'Help' button at the top of the image
display. The XDL_VIEW
image display documentation may also be
useful. If there is a positive response to the software then it is my
intention to provide more detailed documentation.
IPDISP Options
Some of the options available in the program IPDISP are available
through the 'User Supplied Options...' item from the drop down menu
obtained by pressing the right hand button at the top of the image
display. The image display object has a facility to add further user
defined options to the display (programmed in Java) and this facility
has been used to add in these IPDISP based options. For more details of
how to use these options you will need to look at the
documentation for IPDISP.
JdlView Developments
Progress is well advanced in producing a Java equivalent of the
XDL_VIEW package. This will enable similar functionality to XDL_VIEW
to be used in Java based (and hence Web based) programs. The overall
look has been somewhat modernised but the basic philosophy of the
package is the same with the important exception that there are no
plans to provide any interfaces to other languages such as
Fortran. The general purpose objects are in place but those required
for showing simulated diffraction patterns, for example, still need to be
written. My current aim is to produce a
ROTGEN like program in the not
too distant future.
I have been using the JdlView objects for some of my own programs at
home (nothing to do with Protein Crystallography). The timescale and
extent of any PX related software is likely to be closely related to
the degree of interest shown. So, if you feel that it will be useful
to you, any feedback from you will be important even if it
is just an email to say
that you are interested in any of the software.
Demonstrations
Four demonstration images are available. As these are stored on the
web server, they may be accessed without having to set up any special
permissions (though you may need to do that if you want to try the
print option).
Lysozyme Image (Large MAR)
Pig Serum Transferrin Image (Large MAR)
Yeast Phosphoglycerate Mutase Image (Small MAR)
Wax Rings Image (Small MAR)
Image Display Program
A trial program is available in two forms. In the first case the
applet and image display are contained within the Web page. In the
second case, a two button applet is used to launch (or remove) an
independently positioned version of the image display program. Because of the
security surrounding applets, the user will need to set up a policy
file to enable access to the user's image files which are to be
displayed (and printer if required). In addition to the image file,
the user will need to supply an IPDISP type 'spdfil' file name or code
indicating the image type. The following codes are available for
hardwired image type options:
ab 2x2 ADSC scanned binned mode
a 2x2 ADSC scanned
m, ma, mar, MAR image plate scanner
mo, bo
M, bm, ms MAR image plate scanner (squashed pixels)
mc MAR CCD scanner (130 mm)
md MAR CCD scanner (165 mm)
r Raxis 2 fine scan
rc Raxis 2 coarse scan
r4 RAXIS 4 (100 micron)
pf Photon Factory Weissenberg plate
c, C Mac Science 2500x2500
d3 Mac Science DIP2030 3000x3000
d4 Mac Science DIP2040 4000x4000
dc D2AM CCD scanner
px Oxford PX210 CCD detector
You may need to click the mouse in the I/O window so that it has the
keyboard focus before inputting this information. (The colour of the
'Input Mode' message at the top of the I/O window should change from
blue to black when the window has the keyboard focus)
I only know the minimum about setting up policy files. There is a
'policytool' program supplied with Java to help set these up. The best
I can do for you is to show you the
examples of the files I have set up at home for Windows XP and for
Linux. Because of security restrictions the Java file browser cannot
be used from applets and so I have set up a mechanism to enable
directories/folders to be represented by user selected logical names
(cf the FILM directory that used to be used the Vax at Daresbury for
anyone who may remember that).
Image Display Applet within page
Image Display launched from applet
Contact
campbell_j_w@bcs.org.uk
August 2004