Structural Classification of Proteins

Installing rmscop

This page contains technical information for unix/linux users only. A general overview about using RasMol to view structures in SCOP can be found here.

It is assumed that you have both tcl/tk and RasMol correctly installed on your system. To install and configure rmscop on your computer, follow the instructions. If you have any problem, don't hesitate to contact us.

Download rmscop and save it in a directory in your path (typically, ~/bin).
Edit rmscop to configure it. Search for SITE-CONFIG. There are 4 sections:
1. set pdbdir {</pdb_disk/pdb_directory/>}
  where </pdb_disk/pdb_directory/> is the full pathname to your local pdb directory (if you have one) Use: set pdbdir {} if you don't have local pdb files
  set pdbpref {<pdb prefix>}
  where <pdb prefix> is the pdb filename prefix (i.e. pdb in pdb2cro.ent). It can be empty ({})
  set pdbext {<pdb extension>}
  where <pdb extension> is the pdb filename extension (i.e. .ent in pdb2cro.ent). It can include a compression suffix ({.ent.Z})
2. set rasmol {<rasmol name>}
  <rasmol name> must be the name of your RasMol executable file (usually, rasmol)
3. set ftp parameters (ftpserver, ftpserverdir, ftpext, cmpext)
4. set ftpdir {<tmpdir>}
  where <tmpdir> specifies the full path to an area on your system with write permission. Files that are not found at </pdb_disk/pdb_directory/> will be downloaded and stored at <tmpdir>
Change file protections (chmod 755 rmscop)
Add the following line to your .mailcap file:
application/x-rasmol; rmscop %s
(this file should be in your home directory. If it does not exist, simply create it) You may need to source your .cshrc, .login or equivalent file, and start your web browser again before changes become effective. Clicking on a rasmol icon () from a SCOP classification page should open a RasMol window and show the selected molecule.
If you want to have two structures displayed at the same time, launch (from the shell) rmscop twice. This will open two RasMol windows. Then click on two different rasmol icons (). You should get a window that allows you to choose in which of the two RasMol windows the molecule would be displayed.

Copyright © 1994-2005 The scop authors / scop@mrc-lmb.cam.ac.uk
February 2005