PDB Structures w/ SRS-WWW

Rodrigo Lopez rodrigol at biotek.uio.no
Wed Oct 4 18:23:46 EST 1995


Hello SRS fans (actaully this message is intented for the SRS-WWW managers),

Here follow a suggestion on how to display PDB structures using SRS-WWW. I 
have used this method for quite sometime now and find it adequate for 
visualisation purposes. Presently there are two servers using this method
and they are:

http://bioslave.uio.no:8001/srs/srsc

I will not post the name of the second server here as I don't know if
the manager allows access to PDB outside of his site. I'm sure he will
let us all know if he is an accessible point.

..Errr, and please don't bombard my server (modify yours!). Some PDB
entries are very long and choke the networks.

The first thing to do is to add the following CSH script, which I call 
'showpdb' into your server's cgi-bin directory:

-----------------------------------------------------------------------
#!/sbin/csh -f

while ("$1" != "")
set tst=`echo $argv[1] | tr '[A-Z]' '[a-z]'`
shift

echo Content-type: chemical/x-pdb;
echo

# the following contains the absolute path of where you store
# the PDB distribution files

cat /usr3/PDB/"$tst"

end
------------------------------------------------------------------------

The second thing to do is to edit the hyperlink.sdl file in the 'odd' 
directory of the SRS installation. Look for the line that reads:

#linkcall /id=%FETCH_PDB
    /call="<a href=/srs/srsc?[pdb-id:%s]>%s</a>"

and change/add to:
------------------------------------------------------------------------
#linkcall /id=%FETCH_PDB
!   /call="<a href=/srs/srsc?[pdb-id:%s]>%s</a>"
    /call="<a href=/cgi-bin/showpdb?pdb%s.ent>%s</a>"
------------------------------------------------------------------------
Third, make a new call to 'srssection' and you should be setup to 'serve 
structures' to your users.

In this way links to PDB from say, Prosite, PDBFinder, Swiss-prot, etc...will 
return the PDB entry such that the browser will be able to pass it on to an 
external application. A direct query to PDB will result in the server 
returning the actual PDB record. 

I personally recommend the use of Rasmol/Raswin from R. Sayle. for 
visualisation purposes. But users may use any PDB viewer they prefer (i.e. 
Kinemage, GEMM, Whatif, Atoms, depending on what kind of workstation (PC, MAC, 
UNIX) they have).

For PC and MAC users the result of clicking on a PDB link within SRS-WWW 
should result in the WWW broswers (i.e. Mosaic and Netscape's latest versions)
asking for saving the entry or configuring a viewer. This is fairly straght
forward here so I won't go into it. On a UNIX box, the users .mailcap and/or
mime.types file should contain for example:

chemical/x-pdb; xterm -e /u2/RasMol2/rasmol -pdb %s 

If anyone can come up with suggestions and improvements to this please do so
in this list.

OKDK - Thats all folks!!!


R:)




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