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Command line options
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- -h: gives command line options.
- -v: prints current version.
- -pdb <PDB code>: displays the PDB entry in RasMol.
- -dir <path>: changes execution location to <path> before any other operation.
- -tagdef <keyword>: uses the single word <keyword> to tag a RasMol window.
- -tag <keyword>: sends the commands to the RasMol window tagged with <keyword>.
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RasMol management
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On MS Windows operating system, only one RasMol at a time can be manipulated with RmscopII. This is due to the protocol of communication with RasMol implemented on that OS.
On UNIX and Mac operating systems, multiple RasMol windows can be handled at the same time.
On startup, RmscopII collects the information about already running RasMol jobs and makes them available for further operations. New RasMol windows can be started directly from RmscopII.
When RmscopII receives data to be sent to RasMol, if none or one RasMol is running, the procedure is automatic. When more than one RasMol is running, the buttons will be highlighted in red and you can choose which one will receive the data.
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PDB View
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Direct access to a PDB entry from the interface. Does the same as the '-pdb <PDB code>' command line option.
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Automatic FTP
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If activated in the Preferences, any PDB entry not found on the local disk will be automatically downloaded.
FTP sites:
In europe, use: ftp.ebi.ac.uk/pub/databases/rcsb/pdb/data/structures/divided/pdb
In US, use: ftp.rcsb.org/pub/pdb/data/structures/divided/pdb
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File compression
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Although RmscopII can't handle compressed files as direct input, it can manipulate PDB entries compressed either with the 'compress' or 'gzip' programs. Check the Preferences to activate/inactivate these options.
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Input files
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RmscopII has been designed to recognise as input files either PDB files or RasMol scripts. Remember that compressed files are not supported as direct input.
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Tagging RasMol
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RasMol windows can get a tag (one word only). Tagging a RasMol window can be done using the command line -tagdef <tag> option or in a RasMol script with the first line defined as:
#rmscop: -tagdef|<tag>
If only one RasMol is running, it will get the tag attribute by default. If more than one RasMol is running, the one selected by the user will receive the tag.
To send new commands to a tagged RasMol window, use either the command line (e.g.: -tag <tag>) option or in a RasMol script with the first line defined as:
#rmscop: -tag|<tag>
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