Plasmid ARTIST® V1.2.3r15 Release Notes

Version 1.2.3r15 - 1/22/96

This document describes highlights in the Plasmid ARTIST® User's Manual. This will help you to quickly get started with Plasmid ARTIST® Version 1.2.


Contents


Installation

Plasmid ARTIST® requires System Software version 6.0.5 or newer, and is compatible with Systems up to 7.5 and PowerMac computers (in emulation mode). Installation on a hard disk is strongly recommended. Please note the Authentication Code on the diskette envelope. Keep your Authentication Code in a safe place. You will need it to reinstall Plasmid ARTIST® and for future upgrades. See Chapter One for complete details on system configuration, installation and authentication.

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Importing DNA Sequence Files

Plasmid ARTIST® can read sequence files in four formats: ASCII, ABI ".seq", GCG (University of Wisconsin), and Intelligenetics VAX. You may have to consult your system administrator to learn how to move sequence files from your VAX or UNIX workstation, to your Macintosh. Once transferred to your Macintosh, Plasmid ARTIST® can read these file formats directly. Be sure that you do not add or remove any information from the files as you transfer them. They should end up as TEXT files on your Macintosh. If you have problems, try opening the file with TeachText, a utility program that opens TEXT files.

If you are retrieving Genbank sequences from the World Wide Web (www) then you will need to edit the resulting sequence files before importing them into Plasmid ARTIST®. Use a word processor to open the file, remove all of the leading annotations and any trailing lines such that the file contains only sequence data (numbered lines of sequence are OK). Then save as a TEXT file. The resulting file can be imported as ASCII format.

You can also create ASCII files by typing sequence into a word processor. Refer to Appendix F for allowable IUB characters. Plasmid ARTIST® can interpret any line length you desire. Just make sure that the file contains only IUB characters. Then save the file in Text Only format from your word processor.

DNA Sequence is imported into Plasmid ARTIST® either by using the "New Map from Sequence..." command or by importing it into a fragment using the "New Fragment..." command. Both of these operations are described in Chapters Three and Five.

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Generating Restriction Sites from DNA Sequence

Once you have imported a sequence into a map, use the "Digest..." command to analyze it for known restriction sites. Plasmid ARTIST® searches through your sequence for each of the enzymes you specify and creates a restriction site label for each it finds. You can then use the "Align..." command to tidy-up the positions of the sites. You can also set the font characteristics. See the sections on the "Digest..." command in Chapters Three and Five.

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Editing Enzymes

Plasmid ARTIST® now maintains a library of over 80 restriction enzymes complete with details of their recognition sequences and cut sites. If you find you need to add an enzyme you can use the Enzyme Editor window. The Enzyme Editor is introduced in Chapter Five and adding enzymes is described in detail in Appendix G.

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PICT Files and PICT Clipboard

Plasmid ARTIST® creates PICT graphics for export to other graphic programs. The PICT graphics can be exported by copying the selected map objects to the Clipboard or by saving your map as a PICT file. When creating PICTs, you have a choice between creating high quality images which will give very nice results with slide imaging software, for instance, or a lower quality graphic which is compatible with MacDraw. You choose between these two types of PICTs by using the Preferences command discussed in Chapter Five. Appendix D also discusses issues relating to exporting graphics.

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Compatibility with Version 1.13 Files

Plasmid ARTIST® Version 1.2 automatically reads Version 1.13 plasmid documents. When you attempt to save a plasmid that was created in Version 1.13 from Version 1.2 it will prompt you for a name to save the file with. This serves to remind you that once you save the file in Version 1.2 format, you can no longer use Version 1.13 with that file. Since Version 1.2 automatically reads both old and new file formats, double-clicking any Plasmid ARTIST® document will launch Plasmid ARTIST® Version 1.2 as long as you remove your old version from your hard disk.

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Keyboard Shortcut

When you press and hold the command (apple) and option keys, the pointer will changed to the Arrow (Selection) Tool. This is a handy shortcut which makes it much easier to create maps. For example, when using the Text Site Tool to insert sites, you can momentarily switch to the Arrow Tool to reposition the site.

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PowerMac Compatibility

Plasmid ARTIST® has been tested running in emulation mode on PowerMac 6100, 7100, and 8100 computers. Incompatibilities that have been identified all relate to Extension (INIT) conflicts. If you are having trouble running Plasmid ARTIST® on a PowerMac, try turning OFF the Modern Memory Manager and Restart the computer with all Extensions OFF (hold the Shift key while booting). If this fixes the problem, try removing all Non-System Extensions from your Extensions and Control Panels Folders, or FAX a list of your Extensions and Control Panels to Technical Support.

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Network Problem (program immediately quits)

Some computers will not run Plasmid ARTIST® if the Owner Name and Macintosh Name are not entered in the Network Identity section of the Sharing Setup control panel. Please check your Sharing Setup control panel to be sure this information is entered.

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