Previewing chemfig

Previewing chemfig

[Garreau, Alexandre]

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Hello, I’d like to being able to preview chemfig, like lines beginning
with \chemfig{.

But (a) they’re not detected as LaTeX fragments by the previewer (and it
seems only some matchers are accepted by default, I can’t say, for
instance, “^{\\[a-zA-Z]*[a-zA-Z0-9 ].*}$”), and (b) when previewing I
don’t see any way to include packages, like “\usepackage{chemfig}”, so
that even “\begin{flushleft}<\n>\chemfig{O=O}<\n>\end{flushleft}”, for
instance, doesn’t work.

Is there any way to do this? Otherwise, how could I fix it? Which part
of org-mode to hack? Could this be improved for next release?

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Re: Previewing chemfig

[Nicolas Goaziou]

Hello,

"Garreau, Alexandre" <galex-713@galex-713.eu> writes:

> Hello, I’d like to being able to preview chemfig, like lines beginning
> with \chemfig{.
>
> But (a) they’re not detected as LaTeX fragments by the previewer (and it
> seems only some matchers are accepted by default, I can’t say, for
> instance, “^{\\[a-zA-Z]*[a-zA-Z0-9 ].*}$”), and (b) when previewing I
> don’t see any way to include packages, like “\usepackage{chemfig}”, so
> that even “\begin{flushleft}<\n>\chemfig{O=O}<\n>\end{flushleft}”, for
> instance, doesn’t work.

Have you tried

  #+LATEX_HEADER: \usepackage{chemfig}


Regards,

-- 
Nicolas Goaziou

Re: Previewing chemfig

[Garreau, Alexandre]

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Le 02/11/2014 à 20h45, Nicolas Goaziou a écrit :
> Hello,
>
> "Garreau, Alexandre" <galex-713@galex-713.eu> writes:
>
>> Hello, I’d like to being able to preview chemfig, like lines beginning
>> with \chemfig{.
>>
>> But (a) they’re not detected as LaTeX fragments by the previewer (and it
>> seems only some matchers are accepted by default, I can’t say, for
>> instance, “^{\\[a-zA-Z]*[a-zA-Z0-9 ].*}$”), and (b) when previewing I
>> don’t see any way to include packages, like “\usepackage{chemfig}”, so
>> that even “\begin{flushleft}<\n>\chemfig{O=O}<\n>\end{flushleft}”, for
>> instance, doesn’t work.
>
> Have you tried
>
>   #+LATEX_HEADER: \usepackage{chemfig}

Yes. I think it doesn’t influence the preview system.

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Re: Previewing chemfig

[Nicolas Goaziou]

"Garreau, Alexandre" <galex-713@galex-713.eu> writes:

>> Have you tried
>>
>>   #+LATEX_HEADER: \usepackage{chemfig}
>
> Yes. I think it doesn’t influence the preview system.

It should. Perhaps your Org is outdated.


Regards,

-- 
Nicolas Goaziou

Re: Previewing chemfig

[John Kitchin]

Nicolas Goaziou <mail@nicolasgoaziou.fr> writes:

Interestingly, this:

#+LATEX_HEADER: \usepackage{chemfig}


$\chemfig{A-B-[1]C-[3]-D-[7]E-[6]F}$


exports to pdf correctly, but the latex preview is not correct. All the
letters are jumbled on top of each other.

> "Garreau, Alexandre" <galex-713@galex-713.eu> writes:
>
>>> Have you tried
>>>
>>>   #+LATEX_HEADER: \usepackage{chemfig}
>>
>> Yes. I think it doesn’t influence the preview system.
>
> It should. Perhaps your Org is outdated.
>
>
> Regards,

-- 
-----------------------------------
John Kitchin
Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu

Re: Previewing chemfig

[g Garreau, Alexandre]

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On 2014-11-02 at 22:48, John Kitchin wrote:
> Nicolas Goaziou <mail@nicolasgoaziou.fr> writes:
>
> Interestingly, this:
>
> #+LATEX_HEADER: \usepackage{chemfig}
>
>
> $\chemfig{A-B-[1]C-[3]-D-[7]E-[6]F}$
>
>
> exports to pdf correctly, but the latex preview is not correct. All the
> letters are jumbled on top of each other.

Ok, I tested again, and found that actually any preview (even without
chemfig) completely stops working when I add
« #+LATEX_HEADER:\usepackage{chemfig} », even pure maths. I just get
little shrinked transparent void rectangles.

I’m on Debian Testing (Jessy) and hence use Org version 7.9.3f (GNU
Emacs 24.3).

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Re: Previewing chemfig

[Rasmus]

Hello,

g"Garreau, Alexandre" <galex-713@galex-713.eu> writes:

> On 2014-11-02 at 22:48, John Kitchin wrote:
>> Nicolas Goaziou <mail@nicolasgoaziou.fr> writes:
>> Interestingly, this:
>> #+LATEX_HEADER: \usepackage{chemfig}
>> $\chemfig{A-B-[1]C-[3]-D-[7]E-[6]F}$
>> exports to pdf correctly, but the latex preview is not correct. All the
>> letters are jumbled on top of each other.
>
> Ok, I tested again, and found that actually any preview (even without
> chemfig) completely stops working when I add
> « #+LATEX_HEADER:\usepackage{chemfig} », even pure maths. I just get
> little shrinked transparent void rectangles.

To debug check you *Message* buffer.  You might see something like

   LaTeX errors in `*/tmp/orgtex1687lRq output*'. Use C-c ` to display.

Check the file, compile it, and check that everything works.  Compile it
to dvi and try to run dvipng on the file.

For me, dvipng is unhappy about chemfig since it seems to contain PS
elements.  If I do

    (setq org-latex-create-formula-image-program 'imagemagick)

everything works since it's converted to pdf rather than dvi.

(org-version) => "8.3beta".

> I’m on Debian Testing (Jessy) and hence use Org version 7.9.3f (GNU
> Emacs 24.3).

You might get better results with a recent version of Org.  If you
upgrade to Emacs 24.4 you should get Org 8.2.10, I think.

—Rasmus

-- 
And I faced endless streams of vendor-approved Ikea furniture. . .

Re: Previewing chemfig

[Garreau, Alexandre]

On 2014-11-03 at 01:23, Rasmus wrote:
> Hello,
>
> "Garreau, Alexandre" <galex-713@galex-713.eu> writes:
>> On 2014-11-02 at 22:48, John Kitchin wrote:
>>> Nicolas Goaziou <mail@nicolasgoaziou.fr> writes:
>>> Interestingly, this:
>>> #+LATEX_HEADER: \usepackage{chemfig}
>>> $\chemfig{A-B-[1]C-[3]-D-[7]E-[6]F}$
>>> exports to pdf correctly, but the latex preview is not correct. All the
>>> letters are jumbled on top of each other.
>>
>> Ok, I tested again, and found that actually any preview (even without
>> chemfig) completely stops working when I add
>> « #+LATEX_HEADER:\usepackage{chemfig} », even pure maths. I just get
>> little shrinked transparent void rectangles.
>
> To debug check you *Message* buffer.  You might see something like
>
>    LaTeX errors in `*/tmp/orgtex1687lRq output*'. Use C-c ` to display.

Nothing in *messages*.

> Check the file, compile it, and check that everything works.  Compile it
> to dvi and try to run dvipng on the file.
>
> For me, dvipng is unhappy about chemfig since it seems to contain PS
> elements.  If I do
>
>     (setq org-latex-create-formula-image-program 'imagemagick)

And suddenly, after some trials, everything worked… :D thank you!

> everything works since it's converted to pdf rather than dvi.
>
> (org-version) => "8.3beta".
>
>> I’m on Debian Testing (Jessy) and hence use Org version 7.9.3f (GNU
>> Emacs 24.3).
>
> You might get better results with a recent version of Org.  If you
> upgrade to Emacs 24.4 you should get Org 8.2.10, I think.

Myeah, mixing distribution releases is not always a good idea, but I
think with Emacs it’s fine, and I want so much 24.4 features I’ll
probably do it in little time. 

Re: Previewing chemfig

[John Kitchin]

g"Garreau, Alexandre" <galex-713@galex-713.eu> writes:

I cannot reproduce this, my math previews work fine. just the chemfig is
messed up.

> On 2014-11-02 at 22:48, John Kitchin wrote:
>> Nicolas Goaziou <mail@nicolasgoaziou.fr> writes:
>>
>> Interestingly, this:
>>
>> #+LATEX_HEADER: \usepackage{chemfig}
>>
>>
>> $\chemfig{A-B-[1]C-[3]-D-[7]E-[6]F}$
>>
>>
>> exports to pdf correctly, but the latex preview is not correct. All the
>> letters are jumbled on top of each other.
>
> Ok, I tested again, and found that actually any preview (even without
> chemfig) completely stops working when I add
> « #+LATEX_HEADER:\usepackage{chemfig} », even pure maths. I just get
> little shrinked transparent void rectangles.
>
> I’m on Debian Testing (Jessy) and hence use Org version 7.9.3f (GNU
> Emacs 24.3).
>

-- 
-----------------------------------
John Kitchin
Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu