Mico

starting over: The command \rm is PlainTeX and should not be used in a LaTeX document. Hence, instead of \newcommand{\e}{{\rm e}}, \newcommand{\dd}{{\rm d}}, and \newcommand{\ii}{{\rm i}}, you really ought to run \newcommand{\e}{\mathrm{e}}, \newcommand{\dd}{\,\mathrm{d}}, and \newcommand{\ii}{\mathrm{i}}.

The command \rm is PlainTeX and should not be used in a LaTeX document. Hence, instead of \newcommand{\e}{{\rm e}}, \newcommand{\dd}{{\rm d}}, and \newcommand{\ii}{{\rm i}}, you really ought to run \newcommand{\e}{e}}, \newcommand{\dd}{{\rm d}}, and \newcommand{\ii}{{\rm i}}

Instead of \newcommand{\tr}{{\rm tr\,}}, you should run \DeclareMathOperator{\tr}{tr}.

Your "test document", with an empty document environment, is basically unusable for the task at hand: It contains no \cite, \label, or \ref instructions, and it doesn't load main.bbl. If you think that I have some psychic divination powers, I'm afraid I have to disappoint you bitterly. In fact, I think you should delete the query as you've provided exactly zero actionable information so far.

Since you load mathpazo, it makes no sense to load palatino as well.

I don't understand why you load amsfonts but not amssymb. (amssymb loads amsfonts automatically.)

Unless you do something highly unusualy, you shouldn't have to specify the option dvipdfmx when loading graphicx.

Why do you provide the instruction \newcommand{\bb}{\bibitem} if you use BibTeX to create the bbl file?

Running \baland \eal instead of \begin{align} and \end{align} cannot possibly go well.

The directive \setcounter{MaxMatrixCols}{10} is redundant.

Why did you think that \input{main.bbl} wouldn't work?

I'm still missing a lot of relevant information. For instance, after you uploaded main.tex and main.bbl to Arxiv, did you try to recompile the document? If so, what does the log file say?

If cross-references created by the \label-\ref mechanism aren't getting resolved properly when you compile your document (twice!) on Arxiv, there must be something seriously wrong with your document. Since you've given no information so far about the contents of your document, other than that it employs the revtex4 document class, I'm afraid I'm in no position to speculate what could be going on.

No, I asked if you had removed the \bibliography{...} directive, aka command, aka instruction. (Your document must have included such an instruction when you compiled the document on Overleaf.) I certainly did not suggest you remove the \input{main.bbl} directive. Aside: Why on earth would you consider adding \begin{thebibliography}{...} ... \end{thebibliography} instructions manually?

But did you remove the \bibliography directive (not the \bibliographystyle directive) as well?

If you have an \input{main.bbl} instruction in your document, and if the contents of the bbl file are error-free (possibly a big if), you shouldn't need \bibliographystyle{apserv4-2} at all. Moreover, you shouldn't need the \bibliography directive either. However, depending on how you created the bbl file (on Overleaf, right?) to begin with, it may well be necessary to load the natbib citation management package. You claim that natbib "causes clashes with other packages" -- which other packages? Do please tell us which warning and error messages you get.

Welcome to TeX.SE.

Tex distributions and front ends are distinct.

So, your current TeX distribution is TeXLive2022, and you used pdf(La)TeX to compile the document. Any chance you could update your TeX distribution to either TeXLive2024 or TeXLive2025?

The TeX distribution in use is mentioned on line 1 of each log file. The line might say something like This is pdfTeX, Version 3.141592653-2.6-1.40.27 (TeX Live 2025) (preloaded format=pdflatex 2025.3.11). The inference is (a) that the TeX distribution I'm using is "TeXLive 2025" and (b) that the file was compiled with pdfTeX. (The other two engines in frequent use are XeTeX and LuaTeX.)

Do I interpret your write-up correctly that you're using the by-now ancient version 5.0.2 of TeXmaker? If so, you should go to xm1math.net/texmaker/download.html and download version 6.0.0.

Regarding Q3: Are you unsure which TeX distribution you employ? (TeXmaker is a front-end to a TeX distribution.)

Welcome to TeX.SE.

“I really do not know, why my questions always are reinterpreted.” I’d say it’s because your postings are vague and cannot be acted on sensibly without obtaining some much-needed clarification— which you, for some reason not known to us, steadfastly refuse to provide. Instead, you basically keep asking the same question over and over again. How’s that working out for you?

I'm not a MikTeX user, but I don't think it's necessary to completely uninstall an older MikTeX distribution before bringing it up to date. A complete re-installation may be one way to proceed, but it's not the only one.

I can only recommend that you bring your MikTeX distribution up to the present.

ok, i'm back

I guess not. Am leaving the chatroom now.

@RosieF - Are you there?

Not sure if I understood your final comment correctly. Did you actually update your MikTeX distribution now?

Hi RosieF.

@RosieF - Glad to learn that bringing your MikTeX distribution up to date has solved the problem at hand.

@RosieF - Your claim that "\mathbf fails with Charter" may not be correct -- at least when one compiles one's document with a reasonably up-to-date TeX distribution. (I employ MacTeX2024.) For sure, if I have \usepackage[charter]{mathdesign} in the preamble, then $\dot{\mathbf{b}}^{\mathrm{err}}$ and $\mathbf{b}^{\mathrm{err}}$ both work -- and they both place the superscript term at the correct height. In contrast, $\dot{\textbf{b}}^{\mathrm{err}}$ continues to place the superscript term much too high. Which TeX distribution do you use, and when did you last update it?

@RosieF - I don't believe it's appropriate to use \textbf in math mode. For sure, if one replaces $\dot{\textbf{b}}$ with $\dot{\mathbf{b}}$, the issue of the excessive height of the ^2 term vanishes immediately. Put differently, TeX can "see through" the combined effects of \dot and \mathbf -- but not those of \dot and \textbf -- when it comes to determining where to place the subsequent superscript term.

Why the downvote? Please show me the error of my ways.

@Davislor - You meant to address your comment at user Vinkel, right?

@Vinkel - Sorry, but absent information about your specific typesetting needs, it is very much an opinion-based question. Yes, the LuaTeX engine provides several very useful features -- including the built-in Lua subsystem you mention -- on top of what can be achieved with pdfTeX. However, the extra features also impose more overhead. If your document doesn't need any of LuaTeX's extra features, you may prefer pdfTeX's higher compilation speed.

@Vinkel - I prefer not to answer questions of the type "is vanilla icecream better than chocolate icecream?" -- especially when I have absolutely no information about your specific typesetting needs. :-)

@Davislor - The initial version of the query did not indicate which engine was in use. FWIW, it was me who added the luatex tag, after the OP updated the query.

@Vinkel - unicode-math cannot be used under pdfLaTeX. I reckon that this could be called a problem...

@Vinkel - Please see the addendum i've posted.

@Vinkel - You shouldn't. Don't load either fontenc or inputenc under LuaLaTeX. Instead, load fontspec and issue suitable \setxxxxfont directives, where xxxx could be main, sans, or mono. If your document contains meaningful amounts of math, load the unicode-math package, which, inter alia, automatically loads the fontspec package and provides a macro called \setmathfont.

In the Lua[HB]LaTeX case and default fonts (Latin Modern), please see @Davislor's answer to the query Latin Modern main font with bold small capitals from CMU Serif. You'll need to load the fontspec pacakge and issue a fairly elaborate \setmainfont directive. And, by all means, use \textsc instead of \sc.

@Vinkel - I depends on whether you want to render the entire caption text in small-caps, with "Vinkel" in bold and small-caps, or "Vinkel in small and bold-caps and the remainder in the normal upright font. Not being much of a mind reader, I'll leave the final decision to you.

Why did you change (among other changes) {\mytab{Angle of\\incidence ($^\circ$)}} to {\mytab{Angle of incidence ($^\circ$)}}?

Let me go back to the answer page and post a second addendum.

Do you load the multirow package?

Is it ok if I exit the chat?

:-)

Happily, there's a simple, three-part answer: (a) Load the threparttable environment in the preamble, (b) write \begin{threeparttable} immediately before \begin{tabular}, and (c) write \end{threeparttable} immediately after \caption{...}.