Manuscript Preparation

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Manuscript Preparation

• Using
• Microsoft Word
• Endnote
• LaTeX
• Adobe Products
• Figure Preparation (Post Script)

Brent Mantooth bmantooth_at_psu.edu http//stm1.ch
em.psu.edu/bam
PSU, Chemistry, Weiss Group
This document can be found athttp//stm1.chem.psu
.edu/bam/howto/
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Outline Manuscript Preparation
Using LaTeX Brief overview Using MS Word G
eneral features and interfaces
Adobe Acrobat (and Reader) Copying text and gr
aphics Merging documents Adobe Illustrator
Generating EPS files Figure Preparation File
formats
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Submitting a Manuscript
1. Pick Figures 2. Rough draft 3. Revisions (s
everal weeks) 4. Submit to journal (see each jour
nal for format, page limits, figure format)
5. Wait (weeks to several months)
6. Get reviewer comments 7. Revisions and reply t
o reviewer comments (weeks) 8. Resubmit 9. Wait
(weeks) 10. Receive Galley Prints 11. Approve
Galleys (days) 12. ASAP/web publication (2 weeks
before Press) 13. Press publication (weeks to mo
nths after galleys)
Save every version of your manuscript and every
version of every Figure. Remember you may include
these figures in you thesis and want original
versions.
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Manuscript Preparation File Formats
Journals usually accept manuscripts in only two
formats MS Word .doc files LaTeX .tex files
Figures must be in separate files, not embedded
in documents MS Powerpoint .ppt files are NOT ac
cepted by most journals Acceptable figure for
mats Tiff image format (.tif) Encapsulated Po
st Script (.eps)
check info for authors for each journal
Different journals have different rules
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Software LaTeX
LaTeX is a freeware program designed for
manuscript preparation. http//www.miktex.org/ (
MikTeX is a freeware MS Windows version of
LaTeX) Linux/Unix versions are usually installed
by default (man latex). LaTeX is the preferred
processor for articles that contain many
equations. It is a compiled markup style lang
uage similar to HTML, but made for formatting
scientific documents. A LaTeX document can be c
reated by any word processor or text editor.
Journals provide Style Files that will automat
ically format your document and references to
their specifications. (PSU provides at thesis
style file) LaTeX does have a difficult learnin
g curve, but is the superior method (in my
opinion) for manuscript preparation.
LaTeX can output Post Script or PDF files.
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LaTeX example
\documentclasstwocolumn, 12ptarticle journal
style 2 column paper 12 pt font
\titleExample \LaTeX Document \authorB.A. M
antooth,\thanksAuthor who wrote the paper and
J.B. Nobody \date\today \usepackagegraphicx
used for .eps graphics files
\textheight220mm \renewcommand\baselinestretch
2.0 if this is uncommented it will make the
document double spaced \begindocument \bibliog
raphystyleunsrt \maketitle \tableofcontents \
markrightChapter title or something
\sectionIntroduction This introduction on \LaT
eX begins here. There are a lot of fun commands
to learn, like how to do \it Italics and
\textbfBold face characters. There are other
things such as \emphemphasis.
\subsectionSubsection of the Intro
\LaTeX will take care of most all numbering and
formatting for you, including figure captions and
numbering, equation numbering, and
section/subsection numbering. \beginfigure \
includegraphicswidth1insmiley.pdf
\captionHere is the caption for this really cool
figure \labelfigsmiley \endfigure
\sectionEquations \LaTeX rocks for equation edi
ting, while this looks really confusing, once you
get use to it this is the best equation editor
around. Here is an example equation from my
tracking paper. \beginequation C(x,y) \frac
\sum_i\sum_j(a_1(ix,jy) a_2(i,j))
\left(\sum_i\sum_j a_2(i,j)2\right)1/
2. \labeleqnrealspace this is how you refe
r to the equation from the text
\endequation You can do all kind of equations l
ike this \beginequation \labeleqncorr C_n
(I,J) \cal F-1\left(A_n -
1(I,J)A_n\ast(I,J)\right),
\endequation or in math mode denoted by \, you
can access everything in the equation mode, but
in the text xy2\pi\Pi\Phi\phi. You can
read up on all of the equations that you will
need to use in other books and on the internet.
But just so you know, if I wanted to refer to my
real space equation from above, that would be Eq.
\refeqnrealspace, as named by the label.
\sectionFigures This is one place that LaTe
X can get a little annoying. All graphics MUST
be in post script (ps) or extended post script
(eps). Adobe Illistrator can save graphics files
in the eps format for you, just use the save as
Illistrator EPS format and use level 2 post
script, version 8.0, CMYK colors.
Continued in example file.
Weaknesses Must learn all the commands (or use
LyX, a MS Word like interface to LaTeX)
Strengths LaTeX knows the formatting rules and a
pplies them for you. Equations, citations, and fi
gure numbers are NAMED, LaTeX determines numbers
for you.
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LaTeX Output
Just by changing the \documentclasstwocolumn, 12
ptarticle Parameters, you can switch between
single column draft format or 2 column journal
output. Figures, tables, captions, citations, f
ootnotes are recompiled and renumbered each time
you LaTeX your document. You can change journal
formats from article to the style file provided
by the publishers.
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LaTeX Citations BibTeX
BibTeX is a companion tool to LaTeX that will
format your references. Endnote can export BibT
eX files for use in LaTeX. See Example files fo
r methods to write LaTeX in MS Word and use
Endnote to format .bib files. For more informat
ion on LaTeX and BibTeX see http//stm1.chem.psu.
edu/bam/howto/
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Word - Templates
Download and save the template file (.dot)
Templates are journal specific
They are usually found at the web page for the j
ournal, then look for a link that says
information for authors This should include t
he template and a detailed explanation of how to
use the template and submit a paper to this
journal In general Type paper, highlight text
and push Style button corresponding to
highlighted text.
Example JACS article Template
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Word Applying a Template
1. Open the word .doc file you want to format
2. Open the template window Tools?Templates and
Add-ins 3. Using the Attach button, select the
template you want to use, ex. ACSTemplate.dot.d
oc
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Word Formatting with Templates
For the ACS template the Styles window will
appear Highlight the text to be formatted and s
elect the appropriate button, Ex. BA_Title Style
for the Title.
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Word Dealing with Figures
1. Paste Figure into word doc.
2. Select Figure.
3. Insert?Reference-Caption
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Word Adding a Caption
Type in caption. Dont worry about format (bold)
it can be changed later. You can set AutoCaption
so this will pop up every time you paste
something into word.
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Word Cross Referencing
To reference a figure in the text
Place the cursor in the text where you want the
cross reference to go Select Insert?Reference?C
ross-reference
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Word Referencing a Figure Number
Select the Figure you want to cross-reference.
You may need to select Reference Type to Figure
Select Only label and number in the Insert
reference to box
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Word Figure Numbers
Using this method you can rearrange figures and
figure numbers will auto update
To update figure numbers, press Ctrl a (select
all), then right click on any of the selected
text, then select Update Field
Sometimes it is easier to manually name figures
in your text like Figure CCDSpec, and then
number them just before submission. This helps
to prevent the pains of renumbering an entire
manuscript.
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Equation Editor
MS Word Menu Insert-Object Select Microsoft Eq
uation 3.0
Click OK
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Microsoft Office - Toolbars
Tools ? Customize RClick on any Toolbar ?Customiz
e
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Customizing Toolbars
Click on a Command and drag it to a tool bar
Useful Commands Super (ctrl shft ) / Sub
script (ctrl ) Align top, bottom, left, cen
ter, etc. Distribute horizontal, vertical Strike
through
To get to this dialog box Tools ? Customize RCl
ick on any Toolbar ?Customize
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MS Word Tracking Changes
Enabled/Disabled from Tools?Track Changes
Content is changed, keeping track of deleted and
inserted material. Each author is automaticall
y assigned a color to denote which auth made the
change. New and deleted material can be accepte
d or rejected by any of the authors.
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AutoCorrect as a Shortcut
Type in any acronym or keyword to be replaced
The word is replaced after the word is typed and
the user hits the space bar.
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MS Office Turning off AutoFormat
Applies to all MS Office products
Most annoying features ever Auto bulleted an
d numbered lists Auto layout for inserted objec
ts (rearranges entire slide when you paste s
omething.) If you are using Word to type a LaTe
X document, turn of most all of the format
changes, especially the smart quotes.
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MS Office Show All Menus
MS Office tries to make the menus less
complicated by hiding some contents. This makes
it hard to find some options. To turn this
feature off, check this box.
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Acrobat Copy Graphics
Using the Graphics selection tool
Draw a box around figure and or text that you
want Edit-Copy (CtrlC) And Paste into applicat
ion Resolution is determined by image size on t
he screen Cite everything you copy
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Acrobat Copy Text
Text can be selected and copied
For 2 column papers, use the Column select tool
Cite everything you copy
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Acrobat Modifying pdfs
PDF documents can be edited or modified
You need Adobe Acrobat to edit pdf files Adobe
Reader cannot do this.
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Figure Prep
Journal dependent dimensions but this is ACS
standard Single Column width 3.25 inches Double
Column width 7.0 inches Max Length 9.5 inches
Major accepted formats Tiff Files
uncompressed graphics, large size, can become
pixilated Software Adobe Photoshop, any graphic
s editor EPS Files Encapsulated Post Script
vector graphics, high resolution, small
size, can include any graphics.
Software Adobe Illustrator
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Adobe Illustrator
Very powerful graphics/post script editor
Steep learning curve, CAC offers free classes
Can import and edit metafiles, post script, pdf,
printer files (.prn), any graphics format (bmp,
jpg, gif, tiff), and many more.
True to size imaging (units in inches, pixels, p
icas, etc.) Can save EPS, PS, pdf, or .ai files
. To convert almost anything to a file Illust
rator can read from most any software
Select object, go to File?Print. Select the
check box print to file. This will generate a
.prn file that Illustrator should be able to read
and edit.
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Tiff vs. post script (vector)
Tiff files are stored as pixles, with a fixed
resolution.
Post script, pdf, or eps files are vector
graphics, the objects are stored as lines and
boxes, and text with colors. These graphics can
be rendered at variable resolution, and are often
much smaller files.
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MS Program Short-Cuts
Key Action Ctrl X Cut Ctrl C Copy Ctrl
V Paste Ctrl ? Skip to next word Ctrl Shi
ft ? Highlight this word Ctrl Z Undo Ctrl
Y Redo Ctrl S Save Ctrl B Bold (on/off)
Ctrl I Italics (on/off) Ctrl A Select
All Ctrl Sub Script (on/off) Ctrl Shift
Super Script (on/off) PrtScn Print Screen
Paste a screen shot into photo shop or ppt.