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Plasmid Maker Stack

Each plasmid has its card with

• its name
• its size (base pairs)
• its number in the database
• a list of restriction sites (position enzyme name)
• a list of genes and fragments (begin end name orientation+display options)
• additional information (displayed with button "Plasmid Info")

"Beautify" sorts by position/begin and aligns with spaces (use after electronic "cloning").

The different functions of the stack are accessed via the pop-up menu "Action".

• "Display Plasmid" moves to other plasmids in the stack
• "New Plasmid" requests name and size of the new plasmid. Besides starting from scratch it allows to start from a plasmid present in the stack (accept its size as recommended, it adapts to the size changes by deletions or insertions). "Import" uses the data from a text file: its first lines can contain name and size (separate lines) or just the size. Each restriction site must stand in a separate line as "enzyme name restriction site" or as "restriction site enzyme name", separated by space or by tab.
• "Export Plasmid" exports all data of a plasmid (name, length, restriction sites, genes, additional information) to a text file suitable for import, the easiest way to share the plasmid data or to produce specialized collections (see below).
• "Delete Plasmid" deletes the plasmid card and a hidden reference (so don't use "Delete Card" from the menu) after requesting a confirmation.
• "Enter RE" requests enzyme position and name (move w ith tab key). After data entry (button "Enter"), the position is highlighted for editing, allowing to enter all sites for an enzyme without having to retype the name. The word "Enzyme" above the RE name field is a pop-up menu (hold the mouse button) of the names of restriction enzymes; using it garantees a consistent naming, important for the allocation of stroke lengths when printing (see below).
• "Enter Gene" requests begin and end of an element of the plasmid (e.g. gene or cloned fragment), its name (without spaces, otherwise, only the first word is used), and with which width (1 to 99 points, a point is the 1/72th of an inch) and which grade of gray the element will be drawn (choose from pop-up menu), whether it shall be displayed as a stroke or as a box (black border of adjustable width, filled with gray as specified) and whether the gene shall have an arrow tip and if so, in which orientation (to indicate the orientation of an ORF). If the gene is shorter than 4 times the stroke/box width, no ar row tip will be appended. The list of genes/fragments shows begin and end of the respective element (position in base pairs), its name, and information about the display in the drawn map. "-" symbolizes display as a dash, "=" display as a box, arrow heads are shown as ">" or "<", respectively. For the border of boxes, "/" represents 0.5 point, "|" 1 pt, "|/" 1.5 pts and "||" 2 pts width. The shade of gray is shown as % black. Caution: dashes (but not boxes) of 0% black are invisible.
• "Delete Data" allows erasure of restriction and gene information, for the deletion of several entries hold the option key while clicking the respective data. In addition, "Delete Data" is useful to correct errors during entry or to modify display options: after clicking an entry (without the option key), the data are displayed in the correct entry mode (restriction site or gene), allowing to perform the alterations and to reenter the corrected data.
• "Insert Fragment" allows to enter a new fragment into the plasmid, a nd to copy ("clone") parts of other plasmids with their restriction and gene data. Name, width and pattern for the inserted fragment are asked for, the genes on the fragment keep their information (exception: if a gene overlaps the fragment completely, its display data are ignored and the data for the fragment are used). If a fragment is inserted into a present fragment, the two parts of the later keep their name and display options.
• "Delete Fragment" allows to reduce the size of a plasmid. The requested positions "from" and "to" for deletion as well as for insertion are part of the respective fragment: inserting a fragment 1-5 "at" position 10 moves the inserted fragment into 10-14, the former position 10 is now in 15.
• "Draw Map"
  

  With "Linear Map", the plasmid is drawn as a bar, with "Circular Map" as a circle. The graphics are in the Postscript format Illustrator-EPS. The graphics can not be displayed nor edited within the stack, but printing (on a Postscipt-capable printer) is possible, and, of course, editing in Adobe Illustrator. This will be necessary for most plasmids because the labels of neighbouring restriction sites often overlap and have to be reordered manually.
  Important hint: To keep a definite correlation between stroke and label of each restriction site, the elements are grouped. Ungroup to move the label while leaving the stroke in place (Illustrator can do that for all groups simultaneously with command-a command-u) or for each site separately.
  In the linear display the plasmid consists of dashes and boxes of different widths; restriction sites are marked by cross-lines with the name (and position, if requested) centered above.

  Unedited circular plasmid map (screenshot from Illustrator display)

  

  Edited circular plasmid map (screenshot from Illustrator display)

  
  BTW, a screenshot is a fairly fast way to get a nice PICT file of your plasmids, expecially if you use the control panel "Flash-It" (Shareware from Nobu Toge) which lets you select parts of the screen (just the plasmid). If you organize your plasmid collection using my stack "Plasmid Collection", you can link these pictures to the corresponding plasmids for display within the collection.

  User defineable are
  

  • the scale of the map, in points per 1,000 base pairs, default are 50. More than 700 points fit on a page in landscape orientation, e.g., a 7,000 bp plasmid with 100 points per 1,000 base pairs. If no scale is specified, the program calculates (and displays) it for a landscape page with a small reserve for overhanging labels.
  • the stroke lengths for each restriction enzyme individually (pop-up menu). Enzymes without this information get the "Other" value. The lengths data can be altered, enzymes can be deleted and more enzymes can be added. The intention of these options is to allow to minimize the overlapping of RE labels. Watch the relation of stroke lengths to the width of the plasmid element. If the later is as thick or thicker as the former, it hides it completely, and possibly even its label.
  • the width of the plasmid dash where no gene or fragment is specified (default 5 pts).
  • whether restriction sites are labelled with or without position ("HindIII (3245)" or "HindIII").
  • whether the names of genes/fragments are shown below the corresponding elements.
  • whether a scale bar is displayed.
  • whether name and length of the plasmid are displayed
  • More options, especially concerning the vertical distances of the various elements, are listed in the button script. By clicking button "Linear Map" while pressing option and command key, the script is accessed; the modifyable values, all at the begin of the script, are explained by commentaries.
  All information concerning "Linear Map" are valid for "Circular Map" accordingly. Name, size, and scale bar are placed in the inner of the circle. The program chooses a fragment length for the scale bar (100 Bp, 500 Bp, 1,000 Bp,..., 1,000 kBp) which fits into the circle.
  If the scale chosen for the map results in a plasmid which would not fit on a page (radius > 240 pts), the programs gives a warning with the options to continue with the specified values or to have the program scale the circle to fit it just barely on the page (radius app. 223 pts). If no scale is specified, the program calculates a circle of 160 pts radius.

  Unedited circular plasmid map (screenshot from Illustrator display)

  

  Edited circular plasmid map (screenshot from Illustrator display)

  
  Printing of the map files from the stack is only possible on Postscript-capable printers. Button "Print" asks for the file to print, then displays the printing options. Landscape orientation (necessary for linear maps in default scaling) has to be requested explicitly (portrait is the default), for circular maps, both orientations fit equally.

  EPStoPICT is shareware from Art Age Software, it is available from Sumex mirrors (e.g. my favourite mirror site in the Netherlands) and at ftp://users.aol.com/ArtAge/.
  EPStoPICT converts the plasmid EPS files to PICT format, leaving objects as such, so corrections and modifications can be made with, e.g., Canvas or MacDraw. For the best similarity to the EPS graphics, set the resolution to 300 dpi and choose "Emulate PostScript stroking" in the preferences. Otherwise, some elements can become disaligned and the ends of lines look distorted.
  If parts of the picture are cut off due to the conversion (which should only happen if the drawing exceeds a DIN A 4 or US Letter page in landscape view), this can be prevented by opening the EPS file with a text editor and deleting the line
  "%%BoundingBox..."
  (save as "Text only" and convert the file with EPStoPICT). To use MS Word for the editing, the file "EPS/TIFF/PICT" has to be removed from the "Word 'Commands" folder before starting Word, otherwise, Word will recognize the EPS file as a graphics format and does not display it as text.
  EPStoPICT-conversion of EPS files produced with version 1.0 of Plasmid-Maker results in only a small segment of the picture, again caused by the "%%BoundingBox..." line. You can easily do the upgrade to version 1.1 yourself: Open the message box in Plasmid-Maker by typing "Command-M", enter the following line (Copy and Paste) and press return:
  put "%%BoundingBox:-95 130 690 670" into line 19 of field "Header"
  That's all (only the version number remains 1.0).

Problems, weak points, restrictions: