RmscopII Raphaël Leplae © 2000,2001,2002
Release 2.2
P & S
Starting RmscopII
RmscopII arguments
Starting a new RasMol application
Selecting RasMol
Configuring Netscape
Configuring Internet Explorer
Downloading a PDB entry
Starting RmscopII
If RmscopII is properly installed, you should be able to start the program by:
Type from a shell prompt:

On MSWin
Either double click on the rmscop2.bat file:
MSWin RmscopII icon
or type in a DOS shell:

On Mac
Doube click on the rmscop2 'executable' created during installation:
Mac RmscopII icon

From a web page, clicking on a RmscopII compatible link should start automatically the program, see Browser configuration for more details.

A window like this one should appear on screen:
RmscopII windowRmscopII windowRmscopII window

RmscopII features a Preference button giving access to the parameters configurable by the user.

On MSWin:

On Mac:


  • General preferences
    • Terminal: UNIX only, default to xterm, you can change it to your favourite terminal provided that it is compatible with the options: -geometry 80x10+10-10 -fn 6x10
    • RasMol: default to
      • rasmol on UNIX
      • raswin on MSWin
      • none on Mac. Use the Select button to pick the RasMac application provided with the RmscopII distribution
      Change to the appropriate RasMol executable.
    • MacGzip: Mac only, use the select button to pick the MacGzip application.
    • Rmscop local server port: UNIX and MSWin only. Default to 32160 and shouldn't be changed, this is the port number used to communicate with the RmscopII server.
    • Nb of ports: UNIX and MSWin only. Default to 20. Used to search a free port, starting from 32160, when the server starts on a machine with other RmscopII servers running.
    • Network parameters: select one of the Slow, Medium or Fast internet conection speed based on your hardware.
  • PDB FTP server
    • Automatic download: if activated, RmscopII will automatically try to download a PDB entry not found locally.
    • Address: FTP server address, default to ftp.ebi.ac.uk, change it to a closer server if needed.
    • path to PDB: path to the directory where are stored the PDB entries. Default to /pub/databases/rcsb/pdb/data/structures/divided/pdb, if you change it, be sure to specify the path where the PDB entries are stored in the CDROM style directory tree!
    • Email for anonymous login: default to rmscop@rasmol.user, change to your email address please.
    • File compressed as: type of compression applied to the PDB files stored on the ftp server. Default to .Z, change it to the appropriate type if needed.
    • cache files in: directory where the downloaded files will be stored. Use the Select button to pick a directory.
  • PDB local
    • Stored as CDROM tree: if enable, will treat the PDB directory as a CDROM like tree (the two middle characters of the PDB code used as subdirectory names).
    • PDB path: path to the local copy of PDB. If the system variable PDB or RASMOLPDBPATH is defined, will be the default. Change it to the appropriate path.
    • Files compressed with:
      On UNIX: select Nothing to keep downloaded files uncompressed, gzip or compress to compress them with the respective program.
      Note: no check is made for the availability and location of these 2 programs.
      On MSWin and Mac, only the gzip program is used for compression.
    • File name components: parameters required to rebuild the file name from the PDB code. Default is no prefix and .brk as suffix. If files are compressed with gzip/compress, do not add the .gz/.Z extension, it will be done automatically.
  • Save: will save the preferences in the ~/.rmscop file.
  • Close: will close the Preferences window.
Note: any changes will be immediately applied to the current session even if not saved!
RmscopII arguments
UNIX and MSWin only as MacOS earlier than version X doesn't have a command line feature. The basic command line to start RmscopII is:
rmscop2 <file name>

where <file name> is a PDB or a RasMol script file name to be sent to a RasMol application.

Extra arguments are:
-v Display the program version and exit.
-h Display a brief description of the program and exit.
-pdb <code> Send to RasMol the PDB entry corresponding to the PDB code. If the file is not present locally, it will be ftped (provided that automatic download is activated).
-tagdef <name> The next RasMol button selected will be tagged with <name>. The tag name must be a single word.
-tag <name> The file will be sent to the RasMol window tagged with <name>.
-dir <path> Constrains RmscopII to move is the given directory. This is a convenient function to access RasMol scripts stored in a specific directory. For example:
rmscop2 -dir /cdrom/Rmscripts script1.rmscript
will make RmscopII move in /cdrom/Rmscripts and load script1.rmscript in that directory.
To pass arguments in a RasMol script, add in the script as first line:
# rmscop: -tagdef|TagName
The # rmscop: part will be recognized by RmscopII and the | separated arguments will be used in RmscopII. For example, this can an easy way to assign or direct a particular script to a particular tagged RasMol window.

Starting a new RasMol application
This is for UNIX and Mac only.
To start a new RasMol application, just click on the button.
A new RasMol window should appear on screen and RmscopII will display the associated RasMol button:

If the "RasMol" command line defined in the Preference refers to an incorrect RasMol application, an error message will be issued.
In case RasMol was not started properly, RmscopII will complain about the fact that it couldn't catch the new RasMol window. This might happen if your system is too slow to start RasMol (for example if the executable is located on a remote disk and the network connection is too slow). In that case, start RasMol manually in a shell, the next file passed to RmscopII will trigger the new RasMol detection and the associated button should appear in RmscopII.

Check also the Problems and solutions page for more info about RasMol not being properly recognised.

Selecting RasMol
This is for UNIX and Mac only.
When RmscopII receives a file to be sent to a RasMol window, all the buttons will be highlighted in red (on Mac, the button colouring might not work) telling you that you have to select one of them to display the file content:
All you need to do is to click on one of the RasMol buttons to display the received file to the associated RasMol window.

If only one RasMol is running, RmscopII won't ask anything and will immediately send the data to that window.
Unfortunately, the RasMol window will not be raised on the screen with UNIX, therefore if it is hidden below other windows, you'll need to search it. On Mac, the selected RasMol window will be put on top.
Viewing a PDB entry
The button PDB view allows to view a specific PDB entry based in its 4 letters code. After clicking on it, the following window will be presented:

PDB code field

Enter a 4 letters PDB code and press the <Return> key or the View button. If necessary, the PDB entry will be first downloaded if not present on the local disk and then displayed in RasMol.

Downloading a PDB entry
Provided that the RmscopII preferences are set properly, if the program needs to access a PDB entry that is not present on your local copy of PDB, it will try to download it from the FTP server and a window like this one should appear on screen:

Also by using the -pdb <pdb code> command line option, you can easily download a PDB entry that is not on your local disk.
The download window should display the percentage downloaded at any moment and the progress bar (red) should fill the window at the same time.
Once the download is completed, the window will be automatically closed and the newly downloaded file will be used for display in RasMol.
The caching system will automatically reuse the downloaded PDB file the next time it will be required, provided that it is still present in the cache directory.
The bottom part of the window shows messages returned by the server.

Note: the FTP client is quite simple and might not handle properly all sort of errors due to connection or FTP server problems. If the file is not downloaded properly the first time, you might need to check if the preferences are correctly defined and possibly try a second time. If nothing happen after a few minutes, you might need to kill the RmscopII process and start it again.

Configuring Netscape
The description is related to Netscape version 4.x.
Warning: it seems the same configuration on Mozilla doesn't work and no solution have been found yet.
Open the Netscape preferences (Edit menu, Preferences... option), expand the Navigator tab and select Applications option. The right part should present a window like this:

Click on the New... button, a window will be presented with a number of text fields to be compiled with the following information:

  • Description: Rmscop
  • MIMEType: application/x-rasmol
  • Suffixes: pdb,brk
  • Handled By: select the Application toggle button and enter in the text field rmscop2 %s. On Mac, use the Browse button and select the Rmscop2Droplet provided with the RmscopII package.
Once completed, you should get something like this:

click on the OK button, a new entry should be added in the list of applications and looks like this:

Rmscop        rmscop2 %s
click on the OK button to close and store the preferences.

Configuring Internet Explorer
The description is related to IE version 5.x.
Apparently, Internet Explorer doesn't have an option to define the mime-types, however the MSWin operating system does...
Open any folder using IE (not the Explorer file browser!) and select from the menu View the Folder options... option. In the new window, select the File types tab, you should get someting like this:

To add a new mime-type, click on the New Type... button:
And complete the form with:
  • Description of type: RmscopII
  • Associated extension: .rmscop
  • Content Type(MIME): application/x-rasmol
  • Default Extension: .rmscop

For the actions, click on the New... button and fill the new window as folowing:

Click Ok when completed. In the New Type... window, you can assign the RasMol icon by clicking on the Change Icon... and use the Browse... button to go and pick the RasMol application.
Also in New Type... window, the Confirm open after download option can be disabled so that every RasMol script downloaded will be automatically opened in RasMol.
Once completed, click the Ok button. Repeat the same operation to associate other file extensions (.pdb, .brk, ...) or mime-types (application/x-chemical, ...).

Note: if the Chime plugin is installed it is very probable that IE won't work with RmscopII on the web, but Netscape will.