RmscopII Raphaël Leplae © 2000,2001,2002
Release 2.2
P & S
RmscopII installation
Step1: download RmscopII
Step2: Tcl/Tk package
Step3: start the installer
Step4: Tcl/Tk check
Step5: programs check and installation
Step6: RmscopII installation
Step7: initialising the preferences
Installation completed
RmscopII requires Tcl/Tk version 8.3 or higher plus a number of extra applications depending on the platform.
On UNIX platforms, it is assumed that all these extra applications are installed and consist in: If these applications are not installed, follow the links and proceed to their installation.
On MSWin and Mac platforms, the RmscopII package contains these applications and therefore there is no need to download them.
The RmscopII package features an installer which will be responsible to install and configure the program. The installation is a step-by-step procedure which is described here.
Step1: download RmscopII
If you haven't done it yet, download RmscopII now. Select the platform you want RmscopII to run on and once downloaded, go back to this page.
Step2: Tcl/Tk package
If you haven't installed Tcl/Tk version 8.3 or higher, download and install it now. For UNIX and MSWin, get it from the Scriptics web site.
For MacOS 8.x and 9.x, it is recommended to get it from the SourceForge web site.
Once downloaded and installed Tcl/Tk, come back to this page.

Two notes about Tcl/Tk:
1) Tcl/Tk is quite easy to install, provided basic experience with computers. On MSWin and Mac, an installer will take care of the job. On UNIX platforms, the compilation and installation is straightforward under most operating systems.
2) Most Tcl/Tk scripts written under an earlier Tcl/Tk version are most likely compatible with newer versions.
Step3: start the installer
Go in the RmscopII directory extracted from the archive file you downloaded.
Execute the installer by typing on the shell:
wish install.tcl
On MSWin:
Execute the installer by double clicking the install.tcl icon.

On Mac:
Execute the installer by double clicking the Install icon.

The installer should start with the following window:

If you get an error message, it is probably due to an invalid Tcl/Tk version, check with your system manager.
The Next button at the bottom right part of the window will be green when the installer is be ready to move to the next step.
Note: on Mac, Tcl/Tk can't properly allocate colors to buttons.

Read the text and press the Next button.

Step4: Tcl/Tk check
The installer will check your environment for the Tcl/Tk installation.
On UNIX and MSWin, all possible tclsh executables available will be gathered and you'll be asked to select which one to use:
Select the most recent version and click Ok. On UNIX systems, the non versioned executable is generally a link to the latest version and therefore should be the one to select.
For example if the latest Tcl/Tk version is 8.3, then the /usr/local/bin/tclsh file is often a link to /usr/local/bin/tclsh8.3 executable.
To check this, type in the shell:
file /usr/local/bin/tclsh
the response will tell if it is a link and to which file.

In this figure, the file /nfs/ozone/pdb/IRIXbin/tclsh is a symbolic link to the file /nfs/ozone/pdb/IRIXbin/tclsh8.3 and therefore will be selected as the default Tcl commands interpreter.

The installer will also check the Tcl/Tk configutation. On MSWin, some libraries need to be copied in a specific directory to provide a proper UNIX-like behaviour.
In some cases, it might be necessary to generate the index of some libraries, a necessary step to allow RmscopII (and other Tcl scripts in general) to run properly. This step is not performed during Tcl/Tk installation and therefore will be performed here if necessary. On UNIX systems, that step probably requires root privileges. If you don't have these privileges, ask your system manager to perform the installation.

On Mac, you just need to select the 'Drag and Drop Tclets' application located in the Tcl/Tk installation folder:

Be sure to pick the right application.
'Drag and Drop Tclets' () is found in the 'Build' sub-folder:

Once completed, press the Next button.

Step5: programs check and installation
This step will check if the external programs required by RmscopII are installed and on MSWin systems, the installer will provide the option to install them automatically.
The programs are RasMol and Gzip
On UNIX, if these programs are not found, you will be asked to install them. If both are properly installed, a window like this will be shown:
Select path

On MSWin, if the executables are not found, you will be asked in which directory to install them:
Select path The selection represents all valid pathways where programs can be installed. Select the most appropriate path and click Ok.

On Mac, RmscopII is distributed with the RasMac and Gzip programs. Just ensure that the two folders containing these applications are present in the distribution.

Once completed, press the Next button.

Step6: RmscopII
The installer will now install the RmscopII program.
On UNIX and MSWin, the installer will propose the pathways defined by the system where applications are automatically found. If RmscopII was not installed previously, select the pathway where it will be installed:
Replace RmscopII

If RmscopII was already installed, the installer will display its location and you will be asked to select which one needs to be replaced. Ideally, only one copy should be found. If more than one copy is shown, the first one is most likely to be the one used from the shell command line. To know which copy is used from the command line, type in a UNIX shell:

which rmscop2.tcl
which rmscop2
If a path is given, select the same path in the installer and click Ok

Select RmscopII path

On Mac, the 'Drag and Drop Tclets' selected in the previous step will be used to generated the RmscopII 'executable'. Click on the proceed button to perform the action:
Execute Drag and Drop Tclets Read carefully: if the 'Drag and Drop Tclets' is used for the first time, the program will ask you (check message on top left side of the screen) to 'Select "Wish" stub to clone'. Use the file browser to select the 'Wish' application located in the Tcl/Tk folder: Wish application under Mac
Once selected the 'Wish' application, click on Ok and the normal procedure will continue.
The 'Drag and Drop Tclets' is now asking where to store the RmscopII application. In theory, you could store it wherever you want with the name you prefer. In practice, I would recommend to store it as 'rmscop2' application in the RmscopII folder. An icon like this one will be created:
Mac RmscopII icon

Shells and browsers interface:

On UNIX systems, a shell script called rmscop2 will be generated in the same directory the RmscopII script is installed.
On MSWin systems, a batch file called rmscop2.bat will be generated in the same directory the RmscopII script is installed.
On Mac, an AppleScript called Rmscop2Droplet is provided with the package.

For UNIX and MSWin, be sure to have write permision for the selected path otherwise ask your system administrator to perform the installation.
Click on the Yes button to peform the installation of RmscopII.

The rmscop2/rmscop2.bat file installed with the RmscopII Tcl/Tk script is the one to be used to start RmscopII as it will have all the information to run the program properly.

On UNIX, you'll call RmscopII by typing in a shell:

rmscop2 <with eventual arguments>

On MSWin, you'll call RmscopII either by typing in a DOS shell:

rmscop2 <with eventual arguments>
or by double clicking the batch file icon:
Batch file

On Mac, you start can start RmscopII by double clicking on the rmscop2 executable icon:
Mac RmscopII icon
The Rmscop2Droplet provided with the package as:
Rmscop2Droplet icon
allows to drag and drop PDB files or RasMol scripts on it and to integrate RmscopII with the web browsers (see the Documentation page for more info).
The Installer will execute the Rmscop2Droplet after you click on the Proceed button. A window like this will be shown:
Rmscop2Droplet Use the Set RmscopII path button to pick the RmscopII application you just created previously. Once completed click on the Done button. Now the Rmscop2Droplet will be able to execute RmscopII whenever needed. To change the path later on, just double click on the Rmscop2Droplet.

Once completed, press the Next button.

Step7: initialising the preferences
All the preferences can be defined with the RmscopII application, however the installer will ensure that the basic ones will be defined now.
If the preferences are already defined from a previous version, this step will not take place.
The first question asked is the location of your local copy of PDB. If you don't have a local copy of PDB, just leave the text field blank.
Setting PDB dir If the PDB system variable is defined, it will be automatically used as proposal. If you don't have a local copy of PDB, specify a location where new PDB files will be stored after download.

Next, you'll need to select a cache directory that will be used to store temporary files. If you don't have a local copy of PDB, use the same directory as the one defined above. Click Ok when completed.
Setting cache dir

Once completed, press the Next button.

Installation completed
The installation is now complete and RmscopII should be ready to run!
See the Documentation page to learn more about RmscopII and how to configure your browser to use RmscopII with some web sites.