A package for drawing 2D molecules using the TikZ package.

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2
votes
1answer
35 views

Name in chemfig: on rotation it is placed above, rather than below the molecule itself

please consider the following \documentclass{minimal} \usepackage{chemfig, xstring} \begin{document} \definesubmol{allicin}{% % 1 =[::90]S% 2 ( -[::60]% 3 ...
6
votes
1answer
99 views

Chemfig: length and angle of bonds

I've just tried using chemfig for the first time to try and recreate a figure (below). I had a quick look through the manual so see if there was an example that I could adapt to my needs, and this ...
0
votes
0answers
37 views

Saving Chemfig submolecules in a separate file, to be recovered into beamer

Please consider the following code \documentclass[t]{beamer} \usepackage{chemfig} \begin{document} \begin{frame} \frametitle{1st frame} \definesubmol{x}{-[:+30,.6]-[:-30,.6]} ...
3
votes
1answer
40 views

Problem with mesomeric effect in chemfig

I'm trying to draw mesomeric effect for a molecule using chemfig I would like to create something like this: From the documentation page (see chapter 11 "Representing electron movements")seems easy ...
4
votes
2answers
75 views

How to move bond position with chemfig package?

I'm using this code to generate chemical structure with chemfig package: \documentclass[12pt,a4paper]{standalone} \usepackage{chemfig} \begin{document} \setatomsep{2.5em} ...
1
vote
0answers
52 views

Numbering of equations in chemfig

This might be a stupid question, but how do I number my equations in chemfig? I've drawn this rather complicated equation in chemfig, but I have no idea how to number it. I was hoping to have it ...
5
votes
1answer
102 views

Chemfig - command arrow - alignment doesn't work

I'm writing my bachelor thesis. I wanted to insert a chemical equation, but the reactant and the product are not horizontally aligned well. I found in Chemfig manual a solution to this problem but ...
3
votes
1answer
58 views

In chemfig, grouping with \color ineffective, unlike \textcolor

Some strange behaviour which contradicts the documentation was encountered when creating a figure of 5-cafeoylquinic acid with chemfig. It is stated in the manual that The atoms are displayed in ...
1
vote
1answer
74 views

Draw molecule charge in latex using chemfig?

I've got a lewis dot structure diagram as seen in the following image: However, I would like to have brackets on the outside to indicate the positive charge, since this is supposed to represent H3O ...
11
votes
2answers
238 views

Ugly bond joints in chemfig

Making my first scientific poster I have noticed that Chemfig does not join bonds in a very aesthetic way (see attached image). How can I avoid the small gaps shown here, and make sure the transition ...
6
votes
2answers
159 views

How to draw counter-ions using chemfig package?

For my thesis I need to draw this: With this code I could get everything except for the counter-ion (shown with red arrow, I do not need the red arrow and the line on the figure). ...
5
votes
1answer
122 views

Ring as a submolecule

Is there a nice way to define a ring submolecule and then reuse it in a bigger molecule (maybe something similar to “chemfig and lego-style molecule construction”? (append one ring after another) I ...
5
votes
1answer
73 views

change fontshape for lewis dot in chemfig chemmacro

I wish to draw a chemical reaction showing a radical chain reaction. I am using chemfig and chemmacros and beamer. beamer uses sans serif fonts which is good for display and less fussy. When I write ...
2
votes
1answer
60 views

Bug in \arrow label?

I am trying to scale a molecule which I have as a label over an arrow in a reaction. For some reason, it seems I can't do it and I always get the following error: Argument of \CF@chemfig@i has an ...
16
votes
3answers
1k views

Plus sign in the middle of a ring

I would like to draw in chemfig the following picture: But I am struggling with the "+" sign in the middle of the circle. Is there a way to draw it? Thank you! What I have so far is this: ...
4
votes
1answer
90 views

How do we mirror a reversible reaction arrow in chemfig

In Chemfig, the reversible reactions are represented with a double harpoon. The top one goes from the left to the right, the bottom from the right to the left. One can rotate this double arrow. But I ...
4
votes
1answer
102 views

chemfig: Colored atoms don't align, and how to draw bonds to an electric charge?

So I want to show the ionic interaction between a molecule and a charged element. But when I use color to highlight a part of the molecule, the bond alignment is no longer correct. The first example ...
2
votes
1answer
86 views

Vertical alignment of molecules

\begin{scheme}[h] \centering %\setcrambond{3pt}{1pt}{1pt} %\setbondoffset{3pt} \scriptsize\chemfig{(-[::60]R_1)(=[::180]O)-[::-60]O-[::-60]-[::60](-[::60]O-[::-60](- ...
2
votes
1answer
77 views

Creating delocalized double bonds in chemfig without tikzset?

I'm trying to create a delocalized double bond, similar to the example given in the chemfig documentation. They suggest using the tikz library package {decorations} to implement this. Before running ...
5
votes
2answers
70 views

Angles in Chemfig

I want to draw this formula using chemfig: This is what I've got so far: \chemfig{Cu^+(-[:180]N**6(-**6(------)--(-OOC-)---))(-[1]N)(-[5]N)(-[7]N)} I don't get the angle from N to Cu+ right. I ...
3
votes
1answer
54 views

How to change the default value bond length to an absolute value in chemfig?

Chemfig allows you to set bond length in the second argument of the bond, like -[,2] (a multiple of 2 to the default value). How to set the value of bond length for an absolute value (like 5mm), ...
6
votes
1answer
113 views

Aromatic rings resized with chemfig

When I want to reduce the size of a molecule drawn with chemfig I usually put a [scale=0.xx] before the argument of the command. However when I deal with aromatic rings this method doesn't work well, ...
5
votes
1answer
132 views

Drawing atomic orbitals upon a chemfig structure

Is there a way to draw an atomic orbital in a chemfig structure? I think you can better understand if you see want I want to get: Here is what I've already done. Any improvement would be appreciated. ...
5
votes
1answer
88 views

How to alter the bond length of a double bond in chemfig?

With the chemfig package, is it possible to alter the bond length of the pi-bond in a double-bond? I know about the \setbondoffset{}-command, but in this case, this does not work. Hope the below ...
3
votes
1answer
62 views

Connecting two rings in chemfig

I've spent literally all day trying to figure out how to make this work and I'm completely stuck. I'm trying to make something similar to from this site and I cannot for the life of me get the ...
-3
votes
1answer
281 views

I need to draw the chemical Structural Formula of Bisphenol A [closed]

I need to draw the chemical structure of Bisphenol A as shown on this page: http://commons.wikimedia.org/wiki/File:Bisphenol_A.svg I've also found this presentation how to do it: ...
3
votes
1answer
66 views

How do I refer in the text to a molecule drawn with chemfig?

I just found chemfig fantastic for drawing even difficult molecules. Now, I have a question: how can I put under the molecule a line with a caption like "Figure #: captiontext" and, even more ...
1
vote
1answer
67 views

How do I selectively change bond length in chemfig?

Hi I am trying to create a triacylglycerol molecule with the chemfig package.. I am pretty close. The backbone has three side chains and double bond off the C atom is running into the previous side ...
5
votes
1answer
95 views

Vertical alignment of atoms in chemfig

I have a problem aligning atoms in chemfig when one of the atoms has a descender. The solution proposed in the manual is not really good, because it changes the position of bonds. Consider the test ...
20
votes
1answer
389 views

Showing pi bonding through chemfig

I've tried to make a diagram which shows pi bonding through chemfig, but I was not successful. Here is what I want. or Since I was unable to do it with chemfig I decided to do it with tikz. This ...
7
votes
1answer
316 views

Drawing Benzene resonance mechanism, and reaction mechanism + curly arrows

I am new to LaTeX and there are few things at which I am stuck. I can draw benzene with alternate double bonds but I don't know how to draw curly arrows to show bond shifting and electrophile attack. ...
13
votes
2answers
570 views

Draw Lewis structures like a book

I want to draw a Lewis structure as in the picture. I tried to do with chemfig but does not perform the separation of the points and a minus in the superscript.
4
votes
1answer
140 views

Anchor point seems incorrect for Chemfig package

I'm trying to use chemfig to draw a basic schematic for enzymatic browning and have encountered a problem. In the bottom reaction (bottom right to bottom left) quinone is formed by the enzyme (denoted ...
4
votes
1answer
177 views

How to annotate this chemical scheme using chemfig package?

To depict a chemical scheme with more than one reactant and more than one product, I used the handy package chemfig. I found some issues though annotating the below chemical reaction in a better way. ...
6
votes
1answer
307 views

How to draw/annotate with TikZ on molecules drawn with chemfig package?

I have just discovered the TikZ spin-off chemfig package for chemistry drawings. I just wanted to add some transparent box to highlight a certain region of the drawn molecule with some text using ...
3
votes
2answers
175 views

Forked arrows with chemfig

How can one make a forked arrow in chemfig? Semantically it is exactly opposite to \merge command but seems like it's not implemented in a package. I don't have any experience with TikZ graphics but ...
1
vote
1answer
161 views

chemfig chemname alignment

I wish to have a reaction in \chemfig and write some details under each molecule so am using the \chemname command. It puts the text under the molecule. However, as I have arrows in the reaction ...
5
votes
2answers
266 views

Fine tuning parentheses inside chemfig

I have the following code: \documentclass[12pt]{report} \usepackage{chemfig} %these for bonds in chemfig \setdoublesep{0.35700 em} % 'Bond Spacing' \setatomsep{1.78500 em} % 'Fixed Length' ...
3
votes
0answers
197 views

Is it possible to use nodes as anchors?

I'm trying to recreate a rather complicated reaction scheme with chemfig and TikZ. For that, I'd like to position several amino acid side chains at specific positions. What I'd like to do is to use ...
3
votes
1answer
74 views

Using \chemabove/\chembelow with \vflipnext

I have a molecule with a \chemabove command in it, and I'd like to mirror it vertically with \vflipnext. Everything is flipped just fine except for the atom positioned with the \chemabove command, ...
4
votes
1answer
140 views

How to line up a chemical structure in the table (chemfig)?

I have a table which has three rows of chemical structures. The structures in the second row are not lined up with the first and third rows. I tried to use \vspace to bring the structure down but it ...
1
vote
1answer
62 views

A hyphen is not displayed in chemfig

I have a problem with a hyphen that is not displayed (according to my pdf file) in a chemical structure (after the arrow, {n}-Bu_4N^+)=-=)), although it is present in the code. My sample code is ...
5
votes
1answer
156 views

Fill the background of functional groups in chemfig

I want to fill the background of some functional groups or atoms including bonds to emphasize them. For instance, to emphasize carbonyl group in a keton, fill the background of C=O like: I'm using ...
3
votes
1answer
80 views

How to cross off the structure with an anchor in chemfig

I am trying to cross of the structure after the arrow (with an anchor) but I get a mess. I've been told how to do that without the anchor. I was trying to move a "cross off" command to different ...
4
votes
1answer
158 views

How to line up the arrow and structure in chemfig

I have the following problems: in the first reaction scheme the arrow is too high and I would like to bring it a little down. in the second reaction scheme the third chemical structure (after the ...
0
votes
2answers
160 views

Latex with chemfig to Word document

I have the following situation: I am writing my thesis in Latex and my adviser, who has never heard about Latex, decided to edit my thesis in MS Word (initially, he made corrections on the printed ...
3
votes
1answer
131 views

Can I annotate the links in chemfig?

chemfig is really great chemical picture editor, but just one problem doesn't allow me to continue the work. In the picture below, you see the chemical picture from the book with numbered links and ...
3
votes
1answer
131 views

How to cross off the structure in chemfig

I do not know how to cross off the structure in chemfig. It should look like on the picture Thanks! Here is my sample code: \documentclass[12pt,doublespacing,letterpaper]{report} ...
4
votes
2answers
164 views

Two arrows in a row in chemfig

I have a problem drawing two arrows in a row in chemfig. I need : A->->B but when I place two arrows, I get a space between them which I don't need: A-> ->B How to fix that? Any help is ...
2
votes
1answer
83 views

Where does the \setarrowlabelsep argument go within the scheme environment in chemfig?

I tried looking in the documentation, but I can't seem to find the exact position for the \setarrowlabelsep in the \schemestart environment of the chemfig package. I would like the label Gpx shifted ...