The script systems described here works exclusively with the (RasMol) protein viewer, since this program is available for the three major computer platforms: unix, macintosh and windows. A more general and versatile communication standard Annmm is under development.
The system is used in scop to specify protein domains and to
highlight the results of sequence similarity searches, referred to as
"visual sequence comparision" (VSC). With
a correctly configured system clicking on any 
icon will cause the specified protein structure
to be automatically displayed with relevant colouring in RasMol on
your local machine. A poster
gives examples of rasmolscripts in use on unix and macintosh
systems.
Getting the rasmolscript system to work does require some setting up to allow the communications between scop and RasMol to work trasparently. If you thing your system might have been configured already by someone else, first try the test scripts.
The scripts here work only on X-based graphical unix workstations and terminals and Apple Macintosh. The basic requirements other than being connected to the internet are:
- Unix
- None (A copy of the PDB database on a local or NFS filesystem is useful, but no longer essential as scripts now include trasparent ftp access).
- Macintosh
- A machine fast enough to run RasMol (68040 or PowerPC) and with > 8M RAM (16M or 8M + RamDoubler) and Netscape 1.1N or later.
- Windows 3.1 and Windows'95
- So far no support for PC's exists, however it should be possible to extend this scheme to PC's, particularly those which have the PDB mounted locally (via nfs, for example) and we would be interested in hearing of any development along these lines. Alternatively consider the Chime interface where plug-ins for PC's already exist.
Obtain and install RasMol if you don't already have it (current
version is 2.5, 2.6 is still beta but quite stable and recommended,
although documentation is incomplete [6/96]).
The complete source
code and user documentation may be obtained by anonymous FTP from ftp.dcs.ed.ac.uk
[129.215.160.5] in the directory /pub/rasmol for 2.5 and /pub/rasmol/v2.6beta/
for 2.6
On unix systems you can check to see if it is installed already
first by typing which rasmol.
A client program rmscript has been written for macinosh, which uses applescript to communicate with netscape and RasMol to transparently download PDB files and display them with appropriate highlighting. The installer will install all necessary files including the applescript runtime environment if required. Included with the installer is the same WWW documentation found here.
Note that this is beta software and that crashes will probably happen due to the combined instability of using it with Netscape, TCP/IP and interprocess communication, particularly with a modem, so save documents before you use it! Also, because applescript is slow and non-native on PowerPC, rmscript is very slow, although this should be acceptable since fetching PDB files from remote sites will be even slower.
Two unix interfaces to RasMol are provided. For the first, very little setup is required, however each time an icon is clicked on a new RasMol window will be created, which will soon become annoying. The second interface requires the programming language tcl/tk to be installed first, which will most likely need to be done by your system manager.
Note that for either interface a copy of PDB on a local or NFS filesystem is required. An unix version of rmscript (the macintosh version of which contains transparent downloading of PDB files from ftp or http servers) is under development.
printenv RASMOLPDBPATH
If it is not defined, define it by adding a line to your
.login file of the form:
setenv RASMOLPDBPATH /nfs/ind1/pdb
which rasmol
If it is not found, but installed, you must add its location to your
'path' by adding a line to your .login file of the form:
set path=($path /directory_of_rasmol )
.mailcap..mailcap in your home directory.
rasmolscript.sh.
If you are unable to write files to any directory in your path, you need to create a 'bin' directory as follows:
Now save the script file rasmolscript.sh tocd # goto home directory mkdir bin # make a private bin directory
~/bin/rasmolscript.sh and make it executable with the
command:
chmod +x ~/bin/rasmolscript.sh
Having created a private 'bin' directory, you must add it to your
'path' by adding the following line to your .login:
cd
cat >> .login
set path=(~/bin $path)
Before the changes to .login become effective it is
necessary to login again. After you have done this, the command:
which rasmolscript.sh
should return the location where you saved the script. If this works
the tests below should now work.
rasmolscript.sh assumes all PDB files on your system
have names as supplied by Brookhaven,
i.e. pdbxxxx.ent. Various institutes, for
historical reasons use a different naming scheme, such as
xxxx.brk. For this particular scheme you will
need to edit rasmolscript.sh accordingly. The file gives
some instructions on how to do this.
rasmolscript.sh also supports transparent FTP
transfer of any file not already in the directory pointed to by
RASMOLPDBPATH. By default files are downloaded from the
Brookhaven Protein Database Server (PDB) and cached in the
/usr/tmp directory on your computer. If you want to
change to either a nearer FTP site or change the directory (for
example so it writes directly to update your PDB directory) you must
edit the configuration settings in rasmolscript.sh.
Once you have got the standard link to RasMol working, you may be wish to try installing the following advanced interface.
The rmscop script simply makes it easier to use scop
and RasMol together - it doesn't allow you to do anything you can't do
currently with a little clicking and typing, so don't struggle with
tcl/tk unless you think its really worth it. Thanks to
Roger Sayle (author of RasMol) for suggesting the tcl/tk interface to
RasMol.
The current version of rmscop has the following
options:
rasmolscript.sh is that
you no longer have to start a new copy of RasMol each time you select
a structure in scop. rmscop communicates directly with
RasMol if it is already running and only starts it up if it is not.
If there is more than one copy of RasMol running, you will be
presented with a set of buttons so you can select which RasMol will
display your latest scop selection. This makes it easy to compare
structures.
rmscop in a terminal window is a
quick way to start a new RasMol with a separate, small xterm
window.
rmscop filename in a terminal window is a
quick way to display a private coordinate file in RasMol, with the
default colouring scheme used in scop.
rmscop however requires you have have
tcl/tk installed on your computer. The
rmscop is a wish script (wish
is a tcl/tk shell). To discover if tcl/tk
is installed on your computer, try typing:
which wish.
If wish is found then a kind system manager has been
thoughtful enough to install tcl/tk on your system. In
this case you can just download the script and away you go.
If wish can't be found you'll have to get
tcl/tk installed first, which may require some effort
depending on your system. Note that rmscop works with
both tcl7.3/tk3.6 and tcl7.4/tk4.0 however
only RasMol 2.6 will work with the latter. The tcl/tk
packages can be found at any good ftp archieve site. Suggested
anonymous FTP sites are: Europe: src.doc.ic.ac.uk/packages
[146.169.43.1]; US: ftp.uu.net/languages/tcl/
[192.48.96.9]. For information about tcl/tk, see the FAQ.
The additional steps to installed this interface are therefore.
tcl/tk.
.mailcap..mailcap in your home directory.
Note: that the definitions in this file are different to those
in the file for the basic interface.
rmscop.
If you are unable to write files to any directory in your path, you need to create a 'bin' directory as described in the basic interface installation section.
rmscop is supplied with similar defaults to rasmolscript.sh and can be edited to configure it for different PDB filenames and to transparently download files from different FTP sites. See here for details.
rsgen.cgi in WWW page [server].
rsgen.cgi
with client program, rasmolscript.sh, rmscop or rmscript [client].
rsgen.cgi calls in WWW documents
to highlight conserved regions, active sites etc in PDB files. A
tutorial on how to do this is in preparation.
The cgi program rsgen.cgi, on the server, expands the
simple structural specifications passed to it into a complete list of
RasMol commands and send this to the client with a MIME tag indicating
it is destined for a rasmolscript client.
The HTTP protocol uses MIME information types. Normal text is the
time type text/plain, and most documents served by HTTP
are of type text/html. A gif image is of type
image/gif. Generally all of this is invisible to users;
the server automatically determines the type of the file and the
client displays it appropriately (e.g., starting up a gif viewer to
show gif images). The RasMol scripts are implemented by (1) adding an
additional MIME type (application/x-rasmol) on the
server, (2) having users add the MIME type to their local MIME file
(~/.mailcap), and (3) adding a client program (rasmolscript.sh, rmscop
or rmscript) to be run when a rasmolscript/x-rasmol
document is received.
Use the following tests to see if RasMol is correctly configured to be used with scop on your system.
To display PDB entry 5pti using RasMol click here (note: an xterm will be created first followed by a RasMol window. This allows you to enter RasMol command line instructions). You should see the backbone of 5pti displayed with beta-strands colored yellow, helices colored magenta and loop regions colored white with a single spacefilling heteroatom (The heteroatom disappears if you click on 'backbone' in RasMol).
To display PDB entry 1tim, chain A, using RasMol click here. You should see chain A colored as above with chain B colored in violet.
rsgen.cgi
was updated to achieve this.