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Generating RasMol animations non-interactively i...

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Generating RasMol animations non-interactively in UNIX

The inability to use the save and write commands in a RasMol script file is a deliberate security feature. There was a concern about the security of using RasMol on the Internet when researchers started e-mailing and FTPing 'untrusted' script files between sites. This was especially true of sites that have configured Netscape to fire up RasMol with a RasMol script file MIME type. Such a script, executed with "rasmol -script <filename>" may potentially overwrite system and user files, for example creating a "~/.rhosts" file on the remote machine. To defend against this threat I decided to disable the save and write command from within RasMol, unless the command "set write true" had been entered interactively on the command line.

The solution to the problem is to run your scripts with:

        rasmol -nodisplay <pdbfile> < <scriptfile>
        cat <scriptfile> | rasmol -nodisplay <pdbfile>
i.e. pipe the commands into stdin, RasMol can't tell that these haven't been generated interactively and allows save and write commands.

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