From: ORANGE::GOLD::WINS%"[email-masked]" 17-AUG-1990 13:30
To: GILBERTD

Date: Fri 17 Aug 90 11:24:24-PST
From: [email-masked]
Subject: plota.readme file
To: "24986::""[email-masked]"""@VXBIO.SPAN

Notes on the compiled versions of the MacPROT package (Peter 
Markiewicz, 1990)

MACPROT
	MACProt consists of a set of programs for analyzing protein 
sequences for secondary structure, chain flexibility, hydropathy, 
helical wheels, and so on. Each program is supplied in a separate 
archive file. A list of the programs is given below.

	These notes on the MacPROT package (compiled) are adapted 
from the original instructions for the interpreted MS basic versions. 
Changes have been made to reflect the differences between the 
compiled and interpreted versions. A reference list will be given in a 
later version of this document. 
	Each compiled version is supplied with the portion of the 
original manual which covers it, and the general descriptions in this 
document.  A complete list of the programs (June 1990) is given 
below.

Differences Between Complied and Interpreted versions:
	The compiled versions are for 512k mac and up models. Note 
that the programs may have problems with unenhanced (64k ROM) 
512k macs. To run (simpler) versions of the programs on an "classic"  
512k mac, you need to get the interpreted versions of the programs 
from Angela Luttke, as well as the Microsoft Basic interpreter.
	The compiled versions are (1)faster, (2)handle several input 
file types, (3) Allow printing of larger output pictures (up to 11", (4) 
allow user control of output file type, (5)allow user control of output 
colors, which will work with color output devices even if the mac has 
a black and white screen, and (6) improved mac interface and 
behavior under MultiFinder. Compiled versions run about 5-10 times 
faster than the interpreted versions.

Using 6-point Monaco
The Plot/A programs will use 6-point Monaco to output, if it is 
available in the System Folder. The font is supplied for installation. 
Using the smaller font makes the output charts easier to read.

Adding to the output picture
The user may add to the output drawing by clicking on it with the 
mouse. If a peak on a hydropathy plot is clicked, for example, the 
program will list the position in the protein that was clicked. This is 
very useful for finding interesting stretches in the peptide sequence. 
The numbers are added to output ONLY until the user saves the 
output to the Clipboard, or prints the result. After that, the user 
cannot add to the existing picture. The numbers are drawn in Monaco 
9-point font UNLESS you have installed Monaco 6-point in your 
system folder. The font is provided for installation with the MacPROT 
package with the compiled versions.

Input File Formats
	The interpreted versions of the programs recognize a specific 
format, and have file errors if any other sequence file format 
(including plain sequence is used). The compiled versions are more 
flexible, and can handle the following formats: the original MacPRot 
format, plain sequence (no comments or numbers), Pearson format, 
EMBL format, GenBank format, and IntelliGenetics format. If the file 
contains more than one sequence in these formats, only the first 
sequence is loaded. In theory, files up to 32,000 amino acids could be 
loaded, but the practical limit is about 1000 amino acids. All 
programs were tested for function with up to 1000 amino acid files. 
	The program uses TEXT or DNA Strider protein files only. If you 
type in your sequences with a word processor or other program, you 
will need to save your sequences in TEXT ONLY format. If you don't 
do this, you won't see your sequence when you press the "load file" 
button!  Consult the manual for your favorite word processor on how 
to save a sequence as a TEXT ONLY file. You CAN read protein files
made with DNA Strider. However, this format is tricky, and if you 
write comments in Strider, the PLOT/A programs won't be able to
tell where the sequence ends and the comments begin! If you must
use Strider files, either remove all comments.

MacPROT and MacDraw/MacPaint
	The programs in the MacPROT package work create useful 
output plots which may be printed, or copied to the Clipboard using 
File menu commands. Once the output is copied to the Clipboard, you 
may start either MacDraw or MacPaint (or similar programs), and 
paste the output graph into a document. You can also paste directly 
into your word processor, but you will probably want to edit the 
output chart somewhat before doing this.
	In MacDraw, the object is pasted as a true collection of draw 
objects, rather than a bitmap, which allows you to customize it by 
color, font sizes, etc. MacDraw output prints at the resolution of your 
printer, 300dpi (dots per inch resolution) for a laserprinter, and 72 
dpi for an ImageWriter. You can also paste into a paint-type 
program, which will create a bitmap at 72dpi, and print at 72dpi 
(even with a LaserWriter!)
	Note that this copy/paste routine works with ALL Mac 
programs. That is, is you select "Copy" in any Mac program, load a 
new program, and select "Paste", the Copied result is pasted. This is 
an excellent way to move data between drawing programs and word 
processors. For example, after "cleaning up" a plot in MacDraw, you 
could select it, copy it, start MacWrite or MS word, and select Paste. 
The chart would become part of your word processing document. 
	Note that very large protein sequences (>500-600 amino acids) 
may exceed the maximum allowed output picture size in some of the 
programs. If this happens, an alert warns the user to reduce the size 
of the sequence plotted. If this occurs, the best thing is to analyze 
several portions, copy the results, and paste each segment's results in 
turn into a single draw or paint document. This works especially well 
with MultiFinder. 

The complete set of programs are listed below.

MacPROT programs listed under the menu 'Programs' in the given 
order.
	MENUPROT	 (NOT IN THE COMPILED VERSIONS!!!!) gives 
an overview on the individual programs and their tasks (not under 
programs, but opened either from the finder or from within the 
programs by using 'CANCEL' or 'Exit' in all other programs; see 
below). It is a reminder on what the programs are doing and helps in 
deciding which program needs be opened for a certain analysis. It is 
useful for the starting user, who is not yet familiar with what the 
programs' names stand for.
	AA.DATA	is for storing and revising a protein sequence. The 
program puts the sequence in the format, which is later used by the 
analysing programs. It can also be used for editing an already stored 
sequence. In addition to storing the plain sequence, an optional 
comment as well as data on amino acid frequency and molecular 
weights are calculated and written to the same file.
	PLOT.A/HYD	analyses the hydropathy (hydrophobicity/ 
hydrophilicity) according to four published hydropathy scales of any 
sequence stored in AA.DATA file format.  The plot can be printed or 
saved to the clipboard for pasting it into a picture accepting program. 
After the plot is completed the same sequence can be analysed using 
different parameters and/or a different hydropathy scale.
	PLOT.A/HYD5	analyses the hydropathy of a given sequence. 
It calculates and plots the hydropathy for  five increasing moving 
averages (spans) simultaneously. The first span and the step for the 
increase is chosen by the user. Saving and printing is done as in 
PLOT.A/HYD.
	PLOT.A/SUM	provides three hydropathy plots for a single 
sequence simultaneously using three different hydropathy scales. 
Saving and printing is done as in PLOT.A/HYD.
	PLOT.A/H3	calculates and plots the hydropathy of up to 
three sequences simultaneously. It can be chosen among four 
hydropathy scales. Saving and printing is done as in PLOT.A/HYD.
	PLOT.A/TMH	calculates and plots the hydropathy. In 
addition each value for the chosen span is evaluated for its 
coordinates in a 'hydrophobic moment' plot and the corresponding 
assignment to the helix type shown. The assignment is also written to 
a disk file in ASCII format. Saving and printing is done as in 
PLOT.A/HYD.
	PLOT.A/HEL	draws a helical wheel of a user selected span 
of amino acids, plots the hydropathy, and calculates the mean 
hydropathy using two scales. Saving and printing is done as in 
PLOT.A/HYD.
	PLOT.A/DOT	plots two sequences (the same or different 
ones) against each other in a dot matrix. Two methods are used, 
which either search for perfect matches (identities) or for similarities 
according to five different score matrices based on (a) accepted point 
mutations, (b) genetic and structural similarities, (c) conformational 
state, and (d) observed substitutions. Saving and printing is done as 
in PLOT.A/HYD.
	PLOT.A/GOR	calculates and plots the preference of each 
residue for four conformations (helix, extended, coil, turn) along the 
sequence. The sequence is written to a file in coded letters according 
to the most likely preference. Saving and printing is done as in 
PLOT.A/HYD.
	PLOT.A/GGR	similarly calculates and plots the preference 
for three conformations (helix, extended, coil) along the sequence and 
writes the evaluation to a disk file. Saving and printing is done as in 
PLOT.A/HYD.
	PLOT.A/STR	searches for up to ten user selected stretches 
of amino acids within a given sequence and plots the respective 
positions found along the sequence. Saving and printing is done as in 
PLOT.A/HYD.
	PLOT.A/FOT	suggests regions likely to be amphipathic. 
Two disk files are created (1) to specify the residue starting an 
amphipathic segment, and (2) to write the sequence in coded format. 
Saving and printing is done as in PLOT.A/HYD.
	PLOT.A/POW	plots the power spectrum of a user selected 
stretch. Saving and printing is done as in PLOT.A/HYD.
	PLOT.A/KAS	determines main chain flexibility and in turn 
antigenic determinants.
	PLOT.A/TSL	translates a DNA sequence.

Paths among programs

Each program can be opened from the finder by double-clicking on 
the respective icon or by starting MENUPROT and then choosing the 
respective program from the menu bar under the 'Programs' menu.

From within the programs a different/same program can be chosen 
at any time during the run by pulling down the 'Programs' menu.

A 'CANCEL' button in the first window provides the option to leave 
the program and go to 'MENUPROT'.

There are two other ways of leaving a program during program 
execution, 'Exit' and 'Quit', via the 'File' menu (see sketch above),  
which also contains the options for saving a plot to the clipboard or 
printing it on a dot matrix printer.

A "Help" button in the input window summarizes program use 
(briefly).

The 'File' menu

	Note that the File menu commands for Open and Save are 
handled differently in the MacPROT package.  The standard Open 
command for an input file is provided by the "load file" button, and 
the programs prompt for the name of an output file to Save if 
necessary.
	Save to Clip	saves a plot to the clipboard for pasting it into 
a picture accepting program (graphs created by programs for this 
manual were saved to FullPaint). This option is available only after 
the the plot is finished. It is otherwise identical to the "Copy" 
command found under the Edit menu of most mac programs. At 
other times during program execution (loading a file, choosing 
parameters, analysis) the option is dimmed. If a plot is saved to the 
Clipboard, you should quit the program (Finder), or switch to the 
program you want to paste to (MultiFinder), and select Paste. It may 
take several seconds, since some of the plots are very complex for 
the mac to draw!  Rerunning the program immediately with the same 
or different parameters erases the current plot and creates a new 
one. 
	Print Picture	prints the plot to any printer. As with 'Save to 
...' the option is available only after the plot is finished. The common 
two commands on paper size and printing options need be answered 
before printing starts. Note that MacPROT program can only draw a 
singel page of output, meaning the plot can't be more than 10 inches 
to print. To print a long plot, select the sideways "landscape" print 
mode in the Page Setup Window.
	QuickPrint	NOTE:THIS WORKS ONLY WITH AN APPLE 
IMAGEWRITER!!!! prints an instant hardcopy of the screen on the dot 
matrix printer (printer must be on!) in 'Standard' quality. Though 
similar to the 'Print Picture' option in 'Standard', it's a quick print 
facility omitting the selection windows for paper format and print 
quality.
	Exit 	closes all files in memory (the running program as well as 
textfiles created by some programs) and goes to 'MENUPROT'. The 
option is available all the time during program execution. It is 
particularly useful, if by mistake the 'wrong' program was opened 
and explanations about the label for the 'right' program are required 
(or a cup of coffee/tea is needed in between?).
	Quit	also closes all open files, but goes back to the Finder 
(done for the day!).

The Options Menu
	The compiled versions of MacPROT have an Options menu, 
where the user may change the colors used in creating the output 
graph, and the output file type. Colors being currently used are listed 
in the input window. The color information is recorded even if you 
have a black and white mac. You can print in color to (1)an 
ImageWriter II with a color ribbon, (2)a HP PaintJet or other color 
inkjet printer with a mac interface, or (3)a color laserprinter. The file 
type option sets the output file format used in creating text output of 
the calculations. When the output file is clicked (it may be necessary 
to open and close its volume/folder first), the mac will use the 
specified word processor to open it. MacWrite,WriteNow, MS 
Word,EDIT, and FORMAT are currently supported.

Access to Programs
	Compiled versions of these programs will will become available 
in 1990. They may be downloaded from the following databases 
using electronic mail or FTP over bitnet, internet, or your local net if 
it has a gateway.

 EMBL:  	 NETSERV@EMBL   GET MAC_SOFTWARE:filename.ext

IUBIO:	  IuBio.Bio.Indiana.Edu       (IP name)
   		129.79.1.101                (IP address)

U Houston:  [email-masked]  (INTERNET/ARPANET)
   		uhnix2!genbank-server        (usenet won't work for much 
		longer)
		SEND MAC hqx-encoded-file-name

America Online: New service summer 1990, consult your manual for 
		details

 send HELP messages to find out how to download the programs. 
from the various servers listed above. They are also available on 
floppies as part of a larger set of public domain programs for 
sequence analysis on the Macintosh from the following address:

	Peter Markiewicz
	Dept. Microbiology, MBI, UCLA
	Los Angeles, CA 90024

To get them on floppy, you must 
(1)send 15 800k initialized floppies with blank labels.
(2)Include a return enveloped, addressed to you, with $2.40 postage 
(US).

If one of the above is lacking, the programs won't be sent. It 
normally takes me 2-4 months to process requests.

Note that you can get the programs MUCH faster by using electronic 
mail and/or online databases listed above. A tutorial on how to use 
electronic mail and online databases is available as a HyperCard 
stack from the above address.