Chemistry Stack Exchange
Chemistry Stack Exchange

Questions tagged [software]

For questions pertaining to software used by chemists for professional or academic purposes.

This tag is intended for questions relating to software used by chemists specifically to perform or expedite tasks related to chemistry (relevant meta discussion). Examples include, but are not limited to:

Questions relating to generic types of software that merely happen to be used by chemists (such as word processors, mathematical/statistical software, etc.) may be more appropriate to ask in a different site.

378 questions
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What open-source software can produce 3D PDF representation of molecules?

Most of the existing software I know (like VMD or Pymol) say that they can be used to create PDF files with 3D representations of molecules: actual 3D models, which you can rotate inside the Adobe Acrobat viewer. However, they all require the use of…
F'x
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Creating energy profile diagrams for publication

Is there automated software to create energy profile diagrams like the ones below? One could use something like Illustrator or Inkscape, but they aren't automated, are expensive (Illustrator), are difficult to use, and wouldn't be practical for…
pentavalentcarbon
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How can I draw metallocenes in ChemDraw?

How can I properly draw the structure of metallocenes (e.g. ferrocene) and similar sandwich compounds in ChemDraw? In particular, two problems cannot be solved with the usual workflow when building a molecule in ChemDraw: How can I draw a bond…
user7951
9
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1 answer

Learning chemistry with software?

I'm interested in learning organic chemistry, and am following a text (Organic Chemistry by Clayden) and an online course. I also have access to ChemBio3D. I feel as though the way chemistry is taught conventionally is more difficult than it needs…
user4779
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How does one export a PDB structure to SVG?

This question is one that I'm wondering whether it belongs here or on Graphic Design SE. All I want is some software that can export a PDB structure of a protein (displayed in ribbons style) or DNA double helix, or a combination of the two, to a…
Josh Pinto
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What library/program can draw molecules in 3D programmatically?

Molecular graphics software is usually interactive. But I am looking for a library or program that would be able to render a given molecule based on the commands from another program. I would like to give it a molecule description, the vantage…
Jennifer M.
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How do I take chemistry notes on Mac?

I am learning Chemistry now, and I want to take some notes that involve huge amount of organic chemistry on Mac. How can I do that? Pages does not seem support scientific use.
Ave Maleficum
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6
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Chemistry Spreadsheet Software?

Are there any chemistry spreadsheet-like software that: Generates 2D structure for the entered compounds (based on name or SMILES) Easy to search and create customized reports (such as similarity search) that preferably runs on linux and is not…
user31208
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How do I get MarvinSketch to use the ACS style of drawing?

I have a Wikipedia account and the people there have a tendency for getting upset over chemical structures that I created using MarvinSketch not conforming to the ACS drawing style. Is there any way to make MarvinSketch use the ACS drawing style?
Josh Pinto
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How to make a CP2K input file with Avogadro?

I am trying to learn to work with CP2K and now need to make its input file. CP2K has kind of adaptor for Avogadro2 but not Avogadro ( I don't know what is the relation between them !). I also tried that adaptor plugin with Avogadro2 but it does not…
Aug
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Software to Draw Laboratory Apparatus

So I am preparing a blog post about chemistry for lay people and I have decided to start talking about the basics. It turns out that it would be super useful to create chemical apparatus on demand to illustrate the post. Such as this one: I…
urquiza
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Halogen bonds in QuteMol

I've been using QuteMol for generating 3D animated molecular images and I've encountered a problem; for some reason that's a complete mystery to me when I create a pdb file for etravirine (using MarvinSketch to create a sdf file and then using…
Josh Pinto
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5
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Convert CIF file to SDF file using free Linux-compatible software other than Avogadro or OpenBabel?

I am trying to convert http://crystallography.net/cod/2236556.cif to a file that I can open in Avogadro without some bonds disappearing. See this crystal structure is of tianeptine hydrochloride, yet many of the bonds are not shown when I open the…
Josh Pinto
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Which thermodynamic ensemble does Gaussian's BOMD functionality sample?

Someone sent me a Born-Oppenheimer molecular dynamics output with the following settings line: # b3lyp/sto-3g BOMD=(MaxPoints=35, Ntraj=1, Update=15, RTemp=298) guess=read geom=allcheck Based on my understanding of the BOMD keyword documentation,…
pentavalentcarbon
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5
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ChemDraw: Automatic Caption with Number for Molecules

When working on some reaction schemes in ChemDraw, I sometimes forget to add text/captions with numbering and align it with my molecules before placing all the molecules in a reaction scheme and aligning that. Now that I already have a scheme,…
Eljee
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