Sciencemadness Discussion Board

Two FREE tools you probably didn't even know you had!

blogfast25 - 22-12-2015 at 06:42

1. LaTex formula rendering tool:

Before:

y=ax^3-5/sqrt(2z)

Huh? Bweurk...


AFTER:

$$y=ax^3-\frac{5}{\sqrt{2z}}$$

Better, you think?

This site's 'best kept secret' is that it is LaTex enabled. The G-ds up the SM Mountain regaled us with this gift but forgot to send the memo!

And wherever you see cool LaTex, just right click on it and steal that code and cut/paste/modify to your lion heart's content. Cool or cool?

2. ChemSketch FREE version:

Ok, this one you need to download. Render those pesky chemical formulas like a PRO:

alpha pinene to terpineol.gif - 4kB

Don't get aga to sing the praises of this unbelievably brilliant piece of FREE (forever) software, because he'll never shut up again!

Look at molecules in 3D, rotating them as if you're holding them in your hand!

Downloads are now MANDATORY for membership of SM**:

http://www.acdlabs.com/resources/freeware/chemsketch/

Plenty video tutorials if you get stuck. Or ask here (within reason).
Quote:
ACD/ChemSketch Freeware is a drawing package that allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP.



** JUST KIDDING!



[Edited on 22-12-2015 by blogfast25]

Praxichys - 22-12-2015 at 07:05

Thank you. I was about to start a thread about this myself.

Is there any way we can get a LaTeX plugin for chemistry? Something as basic as chemfig would be phenomenal and reduce the number of images uploaded.

blogfast25 - 22-12-2015 at 07:16

Quote: Originally posted by Praxichys  

Is there any way we can get a LaTeX plugin for chemistry? Something as basic as chemfig would be phenomenal and reduce the number of images uploaded.


It would be GREAT. But that's top management decision time. Nought I can do about that, personally.

Start a petition? :cool:

blogfast25 - 22-12-2015 at 07:37

Even simple inorganic reactions can be rendered in LaTex, see this template, e.g.:

$$\mathrm{Mg}(s)+2\mathrm{H_3O^+}(aq) \to \mathrm{Mg^{2+}}(aq)+\mathrm{H_2}(g)+2\mathrm{H_2O}(l)$$

Praxichys - 22-12-2015 at 07:41

Of course, but that's child's play compared to chemfig. Have a look at this documentation:

http://texdoc.net/texmf-dist/doc/generic/chemfig/chemfig_doc...

Metacelsus - 22-12-2015 at 07:45

Ooh, let me test it out!

$$E = E_0 - \frac{RT}{nF}*ln(Q)$$

(Thanks, gdflp.)

[Edited on 12-22-2015 by Cheddite Cheese]

gdflp - 22-12-2015 at 07:51

It needs "$$" on each side of the LaTeX code for the forum to recognize it as LaTeX.

And blogfast, you just missed the memo:cool:

blogfast25 - 22-12-2015 at 08:05

Quote: Originally posted by gdflp  


And blogfast, you just missed the memo:cool:


2002, yes, before AD Blogfast25. :D

$$E = E_0 - \frac{RT}{nF}\ln(Q)$$

Look mum, without the 'computer' asterisk!


[Edited on 22-12-2015 by blogfast25]

blogfast25 - 22-12-2015 at 08:09

Quote: Originally posted by Praxichys  
Of course, but that's child's play compared to chemfig. Have a look at this documentation:

http://texdoc.net/texmf-dist/doc/generic/chemfig/chemfig_doc...


100 % no contest. I use chemfig elsewhere.

JJay - 22-12-2015 at 08:25

$$\LaTeX \text{is sexy.} \\ P(i_0 \le x \le i_1) = \sum_{i=i_0}^{i_1} p(i=x)$$

Is there any way to render LaTeX code outside of math mode? That would be required for chemfig.

blogfast25 - 22-12-2015 at 13:47

Quote: Originally posted by JJay  

Is there any way to render LaTeX code outside of math mode? That would be required for chemfig.


I've no idea how that works. Wouldn't they be simply independent scripts?

Etaoin Shrdlu - 22-12-2015 at 14:39

There's an mhchem addon for MathJax, but it appears not to have been implemented on the forum. (At least I can't get it to work in preview mode.)

blogfast25 - 22-12-2015 at 14:50

Quote: Originally posted by Etaoin Shrdlu  
There's an mhchem addon for MathJax, but it appears not to have been implemented on the forum. (At least I can't get it to work in preview mode.)


Great as ChemSketch is, an in-forum chem rendering tool might be lighter on the servers (instead of image uploading by members).

[Edited on 22-12-2015 by blogfast25]

Etaoin Shrdlu - 22-12-2015 at 15:56

There is one, the openmolecules.org system.





I don't know if mhchem for MathJax has structure support but it is nice to just type \ce{2 C6H12O6} and have it come out $$2 \ \text{C}_6\text{H}_{12}\text{O}_6$$

Because that looks like this in normal Latex:
Code:
$$2 \ \text{C}_6\text{H}_{12}\text{O}_6$$


That can be done with normal forum code too but it's still a mess. Reactions are so much easier to type and edit with mhchem. (Inline MathJax support would also be nice but I really have no idea how difficult it is to implement any of this.)

[Edited on 12-22-2015 by Etaoin Shrdlu]

blogfast25 - 22-12-2015 at 17:14

@Etaoin:

Whatever the solution, it'd be nice to have something like that: it seems a little outdated that Anno 2015 SM has nothing in place, when the site is mainly about chemistry.

JJay - 22-12-2015 at 21:20

Quote: Originally posted by blogfast25  
Quote: Originally posted by JJay  

Is there any way to render LaTeX code outside of math mode? That would be required for chemfig.


I've no idea how that works. Wouldn't they be simply independent scripts?


I don't think it would be as easy to set up as just dropping the scripts in a directory....

chemrox - 18-3-2016 at 22:07

chemsketch requires registration and the word "mandatory" is anathema to moi. It just seems to me that limit notation is part of the history and theory and is itself limited as has been mentioned. I guess I'm prejudiced because I use mostly partials. And rarely do physics. But I have explained calculus using the concept of limits and have reminded myself how it all works by writing out the ideas with limit notation.

brubei - 18-3-2016 at 22:58

Let edit all the post !

j_sum1 - 18-3-2016 at 23:09

Quote: Originally posted by chemrox  
chemsketch requires registration and the word "mandatory" is anathema to moi. It just seems to me that limit notation is part of the history and theory and is itself limited as has been mentioned. I guess I'm prejudiced because I use mostly partials. And rarely do physics. But I have explained calculus using the concept of limits and have reminded myself how it all works by writing out the ideas with limit notation.

A bit nonsequential, chemrox. It seems like you are answering several threads at once.

I downloaded and use chemsketch. No registration was required. This might be a recent change. Avogadro is similar but not as powerful.

Limit notation in calculus, or more accurately, analysis -- seems an ok way to write the concept. Or, more to the point, if you understand the concept, the notation is pretty efficient. Beginning with the notation and then trying to insert the concept is a way to introduce confusions, but that is a pedagogical issue and not unique to limits at all.

Liebniz notation does have advantages over function notation but I think I sumarised the position in the other thread.

blogfast25 - 19-3-2016 at 06:44

Quote: Originally posted by j_sum1  

I downloaded and use chemsketch. No registration was required.


Same here: no registration was needed.

[Edited on 19-3-2016 by blogfast25]

The Volatile Chemist - 9-4-2016 at 18:33

I knew about latex because it took forever to load on my old Nokia N800...
I feel like I should know what logP is (one of the things the drawing software claims it can calculate) since I'm in AP Chemistry, but what is it...?

blogfast25 - 9-4-2016 at 18:45

Quote: Originally posted by The Volatile Chemist  
I knew about latex because it took forever to load on my old Nokia N800...
I feel like I should know what logP is (one of the things the drawing software claims it can calculate) since I'm in AP Chemistry, but what is it...?


https://en.wikipedia.org/wiki/Partition_coefficient

But what does AP mean? :)

The Volatile Chemist - 9-4-2016 at 18:56

Sorry, I probably should've googled log(P)...
AP is an American university-in-secondary-school class. In high school, you can tale the AP version of a class after you take the normal version, the AP class covering the class at a first-year-university level. Then, if you take a test at the end of the year and do well enough, most universities you would go to will give you credit for the class as if you took it there.
Sorry for all the weird wording, I was thrown off by having to use the phrase university all the time, because 'college' doesn't mean the same thing in the UK as it does here...

Loptr - 13-4-2016 at 05:00

Another handy tool that is available on the web is Solv-DB, which is a database of solvents and their properties. I use it quite a bit.

http://solvdb.ncms.org/solvdb.htm

Eddygp - 15-6-2016 at 10:49

Very useful tool to avoid (summed up) hours of reference finding:

http://chemsearch.kovsky.net/

Make chemistry equations look different with Unicode

Diachrynic - 1-10-2017 at 02:54

I made a small program (23 KB) to make chemical equations somewhat look better.

It turns this:

2MnO4 - + SO3 2- + 2OH- --> 2MnO4 2- + SO4 2- + H2O

into this:

2MnO₄⁻ + SO₃²⁻ + 2OH⁻ → 2MnO₄²⁻ + SO₄²⁻ + H₂O

by using a bunch of RegEx and Unicode. (Had to increase size a bit 'cause it was kind of small.)

If anyone wants to try it out, here is a download link: http://www.mediafire.com/file/aesa60r6c2w4e41/ChemistryInlin... (Just in case if the upload here does not work.)

If anyone wants to extend it, here is the important part of the source code (language is VB):
Code:
Private Sub Convert() Dim Str1 As String = TextBox1.Text Str1 = " " + Str1.TrimEnd(" ") Str1 = Regex.Replace(Str1, "[<]+[-‒–—―=]*[>]+", "↔") Str1 = Regex.Replace(Str1, "[-‒–—―=]*[>]+", "→") Str1 = Regex.Replace(Str1, "(?<!\s\d*)0(?!\d*[+-]+)", "₀") Str1 = Regex.Replace(Str1, "(?<!\s\d*)1(?!\d*[+-]+)", "₁") Str1 = Regex.Replace(Str1, "(?<!\s\d*)2(?!\d*[+-]+)", "₂") Str1 = Regex.Replace(Str1, "(?<!\s\d*)3(?!\d*[+-]+)", "₃") Str1 = Regex.Replace(Str1, "(?<!\s\d*)4(?!\d*[+-]+)", "₄") Str1 = Regex.Replace(Str1, "(?<!\s\d*)5(?!\d*[+-]+)", "₅") Str1 = Regex.Replace(Str1, "(?<!\s\d*)6(?!\d*[+-]+)", "₆") Str1 = Regex.Replace(Str1, "(?<!\s\d*)7(?!\d*[+-]+)", "₇") Str1 = Regex.Replace(Str1, "(?<!\s\d*)8(?!\d*[+-]+)", "₈") Str1 = Regex.Replace(Str1, "(?<!\s\d*)9(?!\d*[+-]+)", "₉") Str1 = Regex.Replace(Str1, "((?<=\s\d+)[+]|(?<=\s)[+](?=\s*[+-]+)|(?<=\s+)[+]$|(?<=[A-Za-z])[+])", "⁺") Str1 = Regex.Replace(Str1, "((?<=\s\d+)[-]|(?<=\s)[-](?=\s*[+-]+)|(?<=\s+)[-]$|(?<=[A-Za-z])[-])", "⁻") Str1 = Regex.Replace(Str1, "\s+0(?=[⁺⁻]+)", "⁰") Str1 = Regex.Replace(Str1, "\s+1(?=[⁺⁻]+)", "¹") Str1 = Regex.Replace(Str1, "\s+2(?=[⁺⁻]+)", "²") Str1 = Regex.Replace(Str1, "\s+3(?=[⁺⁻]+)", "³") Str1 = Regex.Replace(Str1, "\s+4(?=[⁺⁻]+)", "⁴") Str1 = Regex.Replace(Str1, "\s+5(?=[⁺⁻]+)", "⁵") Str1 = Regex.Replace(Str1, "\s+6(?=[⁺⁻]+)", "⁶") Str1 = Regex.Replace(Str1, "\s+7(?=[⁺⁻]+)", "⁷") Str1 = Regex.Replace(Str1, "\s+8(?=[⁺⁻]+)", "⁸") Str1 = Regex.Replace(Str1, "\s+9(?=[⁺⁻]+)", "⁹") Str1 = Regex.Replace(Str1, "\s+(?=[₀₁₂₃₄₅₆₇₈₉]*[⁺⁻])", "") TextBox2.Text = Str1.TrimStart(" ") End Sub


To anyone better in programming this probably looks horrible ;)

Have fun!

Cheers

Attachment: ChemistryInlineFormula.exe (23kB)
This file has been downloaded 1515 times

VSEPR_VOID - 17-5-2018 at 09:44

$$2 \ \text{C}_6\text{H}_{12}\text{O}_6$$
test

[Edited on 17-5-2018 by VSEPR_VOID]

MJ101 - 14-6-2018 at 14:41

Hi,
I found this, which may also be of some use.

https://chemapps.stolaf.edu/jmol/jmol.php

I hope it's of some use to everyone. :)

https://chemapps.stolaf.edu/jmol/jmol.php?model=2595-97-3&am...

fusso - 14-6-2018 at 14:58

Quote: Originally posted by j_sum1  
Quote: Originally posted by chemrox  
chemsketch requires registration and the word "mandatory" is anathema to moi. It just seems to me that limit notation is part of the history and theory and is itself limited as has been mentioned. I guess I'm prejudiced because I use mostly partials. And rarely do physics. But I have explained calculus using the concept of limits and have reminded myself how it all works by writing out the ideas with limit notation.

A bit nonsequential, chemrox. It seems like you are answering several threads at once.

I downloaded and use chemsketch. No registration was required. This might be a recent change. Avogadro is similar but not as powerful.

Limit notation in calculus, or more accurately, analysis -- seems an ok way to write the concept. Or, more to the point, if you understand the concept, the notation is pretty efficient. Beginning with the notation and then trying to insert the concept is a way to introduce confusions, but that is a pedagogical issue and not unique to limits at all.

Liebniz notation does have advantages over function notation but I think I sumarised the position in the other thread.
The registration screen do occur to me

2018-06-14 23_56_25-Program Manager.png - 213kB

Diachrynic - 2-10-2020 at 07:57

Following up on my post from - what the shit pretty much exactly three years ago?! - I have improved the program into something far more practical.

Which one of these two looks better you'd say:

Cr2O7 2- + 2 OH- -> 2 CrO4 2- + H2O

Cr2O72- + 2 OH- → 2 CrO42- + H2O

Using the internal sub- and superscript button is a bit painful tho, especially because you get a dialogue box every time. I wrote an autohotkey script that converts the top line to the bottom line with one key press.

Here is the code:
Code:
#NoEnv ; Recommended for performance and compatibility with future AutoHotkey releases. ; #Warn ; Enable warnings to assist with detecting common errors. SendMode Input ; Recommended for new scripts due to its superior speed and reliability. SetWorkingDir %A_ScriptDir% ; Ensures a consistent starting directory. ^j:: temp = %clipboard% SendInput, {Ctrl down}c{Ctrl up} Sleep 10 Str1 = %clipboard% Str1 := " " + RTrim(Str1, " ") Str1 := RegExReplace(Str1, "[<]+[-‒–—―=]*[>]+", "↔") Str1 := RegExReplace(Str1, "[-‒–—―=]*[>]+", "→") Str1 := RegExReplace(Str1, "(?<![\s\d])(\d+)(?!\d*[+-]+)", "[sub]$1[/sub]") Str1 := RegExReplace(Str1, "(?<=(\s|[A-Za-z]))(\d+[+-]|[+-](?=\s+[+↔→])|[+-]$)", "[sup]$2[/sup]") Str1 := RegExReplace(Str1, "\s+(\[su[bp]\])", "$1") Str1 := LTrim(Str1, " ") clipboard := Str1 SendInput, {Ctrl down}v{Ctrl up} Sleep 10 clipboard = %temp% return


nota bene: In the code I use the function Sleep 10 which was needed to slow down a bit, otherwise it would paste before it overwrote the old clipboard. You might not need this, but it adds only 20 ms delay overall so I think it is acceptable.

If you have AHK already installed you just need to save this code as .ahk and run it. Currently the keybind is set to CTRL+J as denoted by the ^j:: in the beginning, but you can change this to whatever you want. See this part of the AHK documentation for how other keys are encoded.

To use it, run the script, write an equation, select it, then hit the keybind associated with it. It will store your current clipboard, replace the equation with the sub- and supercripted one and then restore your clipboard.

Hopefully this will be useful for some people!

SuperOxide - 13-6-2021 at 13:28

I just saw this post, and thought ChemSketch may be nice to check out. I'm on OSX, and I looked to see if they had a .dmg I could install, and I saw the phrase "Running ACD/Labs Software on Mac computers is not only possible, it's easy!" on their website, which lead me to their tutorial video: How to Install Chemsketch and ACD/Labs Software on Mac (Demo).

The video literally walks you through downloading/installing an open source virtualization software, setting up a VM instance, installing and configuring Windows 10 Home, and installing their software on that...

Ironic, that's the installation process I go through when something's not compatible with OSX too, lol.

j_sum1 - 13-6-2021 at 21:31

I have to admit to being a fan of Webmo.
I have used Chemsketch and also Avogadro. Chemsketch does not display multiple bonds well. Avogadro is cheap and nasty.
Webmo has a lovely phone app which is worth paying for the upgrade. There is also an online demo version that runs through your browser. Simply log in as guest and you are treated to some lovely and quick to draw molecular modelling.
https://www.webmo.net/demoserver/cgi-bin/webmo/login.cgi

I should add that the phone app version calculates and animates molecule vibrations, which is lovely.

clearly_not_atara - 14-6-2021 at 10:55

I haven't uploaded a whole lot of chemical drawings here, but I usually just use this website:
http://py-chemist.com/mol_2_chemfig/

Being a website, it works just as well on Windows, OS X and Linux. No registration required. You can even extract the PDF output and convert it to SVG if you want to write Wikipedia articles. To do this, you might need to use Firefox; right click on the output image and under the "This Frame" menu, choose "Show Only This Frame". But I have to draw my own arrows if I'm drawing reactions.

Somehow, I have been ignorant of $$\LaTeX$$ rendering here for a while, so thanks.

SuperOxide - 14-6-2021 at 14:21

Quote: Originally posted by clearly_not_atara  
I haven't uploaded a whole lot of chemical drawings here, but I usually just use this website:
http://py-chemist.com/mol_2_chemfig/

Being a website, it works just as well on Windows, OS X and Linux. No registration required. You can even extract the PDF output and convert it to SVG if you want to write Wikipedia articles. To do this, you might need to use Firefox; right click on the output image and under the "This Frame" menu, choose "Show Only This Frame". But I have to draw my own arrows if I'm drawing reactions.


That's pretty neat - Bookmarked it for later.

A bit ago I use to use this thing I found (I think I saw it linked on a NileRed video, or maybe PoorMansChemist, forgot which). And it use to work pretty well, but not some much anymore (the AJAX request keeps getting a 500 ISE error).
The Py-Chemist web app looks more powerful anyways, so that works out :-)

Re: Two FREE tools you probably didn't even know you had!

Colleen Ortiz - 22-2-2022 at 05:03

Hello,
LaTex is an amazing tool to use for all things. I like to use it, especially for documentation. LATEX is a document preparation system, not a word processor, that allows you to create professional-looking documents. It excels in typesetting equations and is well-suited to producing long, structured texts. It is available for most operating systems as free freeware.
If you're used to working with Microsoft Word to create documents, you'll notice that LATEX is a totally different way of working. 'What You See Is What You Get' in Microsoft Word implies that you can see how the final product will look. As you type, the document will appear. When you operate in this manner, you will most likely make modifications to the document's look (e.g., line spacing, font size, etc.) as you type (headings, page breaks, etc.) With LATEX, you can't see how the final product will look. The document will appear as you type it, allowing you to concentrate. Rather than focusing on the look, focus on the content. A plain text file with the extension.tex is a LATEX document. It may be entered in a simple text editor like Notepad, but most users find that using a dedicated LATEX editor is more convenient.