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I would like to know the possible alternative available in chemistry software I've found very useful the big list like TeX or StackOverflow I would like have something similar to find the best chemical software for general propose like drawing structure and simple calculation. Is it possible?

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    $\begingroup$ I think this is a good idea. Furthermore, the question can either be complemented by a chemical visualisation big list (comparing and contrasting software for producing 3D visualisations of molecules, e.g. PyMol, VMD etc.) or the question could be made more general to encompass both schematic representation and less abstract visualisation. $\endgroup$ – Richard Terrett Nov 1 '13 at 11:34
  • $\begingroup$ @RichardTerrett could be 3D and 2D visualization two features of a structure drawing software? Maybe chemical visualization can be embedded in this list, are there pure visualization software? $\endgroup$ – G M Nov 1 '13 at 11:42
  • $\begingroup$ @RichardTerrett think you could draft a basic structure drawing/visualization question with some answers along with the basic skeleton as an answer here? You seem to be pretty good with visualization, so you might be the one who knows how best to go about organizing the post. (we already have a small question draft in bob's answer for structure drawing, though not for visualization) $\endgroup$ – ManishEarth Nov 3 '13 at 14:17
  • $\begingroup$ @ManishEarth - Yeah, I'll give it a go. $\endgroup$ – Richard Terrett Nov 4 '13 at 4:32
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    $\begingroup$ @ManishEarth - Just an update - haven't forgotten about this, have a partial list. $\endgroup$ – Richard Terrett Nov 6 '13 at 9:09
  • $\begingroup$ @RichardTerrett Take your time. Though a partial list is all we need to get started, then we can post it on main and let the community fill in the gaps. $\endgroup$ – ManishEarth Nov 6 '13 at 9:14
  • $\begingroup$ @RichardTerrett In my opinion is important to define the features to list then for the community and the user experience will do the rest... $\endgroup$ – G M Nov 6 '13 at 9:18
  • $\begingroup$ @ManishEarth Can we write here a list of features post as an answer to this question? $\endgroup$ – G M Nov 6 '13 at 9:19
  • $\begingroup$ @GM Sure. What I was thinking was that we would partially draft the post on meta as a community wiki answer here, and then copy it to main later and let everyone collaboratively create it. $\endgroup$ – ManishEarth Nov 6 '13 at 9:20
  • $\begingroup$ @RichardTerrett I've tried design a new template in a new answer... Have you something ready? $\endgroup$ – G M Apr 2 '14 at 11:47
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    $\begingroup$ @GM I'll address this in the coming days - I've been fairly busy recently. I would suggest that the array be formatted in a more subtle way (e.g. remove most of the grid) $\endgroup$ – Richard Terrett Apr 7 '14 at 5:54
  • $\begingroup$ @RichardTerrett take your time, did you see the last answer edited in 2 April? because the last has no grid...Thanks for the help! $\endgroup$ – G M Apr 7 '14 at 7:53
  • $\begingroup$ @GM Okay I'm working on this right now $\endgroup$ – Richard Terrett Apr 11 '14 at 13:27
  • $\begingroup$ @RichardTerrett let me know if there is something I can do, I will be in the chat... $\endgroup$ – G M Apr 11 '14 at 13:30
  • $\begingroup$ I'm for a list, but how do you place it on the site. $\endgroup$ – LDC3 Apr 20 '14 at 22:15
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I've tried some template with $\mathrm\LaTeX$ array for a list in the question:

\begin{array}{lllll} \hline & \text{Type} & \text{Auto Optimization} & \text{Fragments} & \text{Molecule Info} \\ \hline \text{Avogadro} & \text{3D} & \text{yes} & \text{yes} & \text{M.W., IUPAC} \\ \text{BKChem} & \text{2D} & \text{no} & \text{very few} & \text{NOX} \\ \text{ACD/Labs} & \text{2D/3D} & \text{yes} & \text{yes} & \text{M.W., IUPAC} \\ \hline \end{array}

And for the answer:


Avogadro


Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

\begin{array}{ll} \hline \text{Type} & \text{3D} \\ \text{Infos about molecule} & \text{Molecular weight, IUPAC name} \\ \text{Calculations} & \text{Add }~\ce{H}~\text{from}~\mathrm{pH},~\text{Electric potential surface}\\ \text{Platforms} & \text{Windows, Linux, macOS} \\ \hline \end{array}

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    $\begingroup$ This is good, though I think the array could be replaced by a bulleted list :) $\endgroup$ – ManishEarth Jan 9 '14 at 19:47
  • $\begingroup$ I appreciate your work, but I think it's crucial to treat 2D structure editors like BKChem and 3D packages like Avogadro (with force fields for optimization, etc.) separately. Not that both aren't great open source tools ;) $\endgroup$ – Klaus-Dieter Warzecha Jan 11 '14 at 9:02
  • $\begingroup$ @KlausWarzecha Ok, maybe we should make two different list...What I was thinking is that Avogadro isn't a pure computational chemistry package like Gaussian, Gamess is more for visualization rather than computing. $\endgroup$ – G M Jan 11 '14 at 9:56
  • $\begingroup$ @GM I totally agree with you on Avogadro. It's more in the league of Gabedit, means they are nice to prepare input files for Gaussian, Gamess, Mopac. Whether to place pyMol there too I'd leave to others. I've played with it, but I was never a protein guy. $\endgroup$ – Klaus-Dieter Warzecha Jan 11 '14 at 10:11
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    $\begingroup$ I made a post on how web based chemdoodle is used chemistry.meta.stackexchange.com/questions/3736/… $\endgroup$ – Pritt says Reinstate Monica May 23 '17 at 5:30
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I wonder if a format such as the following would work.

Chemical structure drawing software list

What software packages are available for drawing chemical structures? Answers to this question should focus on a single software package and highlight key features, where to download/try/buy, computer requirements (which OS). While it isn't always possible, try to keep opinions and subjective information to a minimum. Rather, advocate for a particular software package by voting up that particular answer.

The Q&A would be a community wiki so multiple contributors can improve the quality of a software package description.

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  • $\begingroup$ Yes it sounds good. Maybe we should try to make a features list to understand what words to use... $\endgroup$ – G M Nov 1 '13 at 8:21
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    $\begingroup$ In my opinion we should provide a "template answer": an answer (or a meta-answer) that one can copy from edit and use to structure his own answer. $\endgroup$ – G M Nov 1 '13 at 9:33
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While the SE model in general is not good for big lists, I think it's OK to have a couple community-maintained ones on frequently asked topics.

(I and @bobthechemist were discussing this in the past, IIRC.)

I'm for this if we can formulate a focused question and maintain a well-organized, Community Wiki answer.

I think two questions — one on drawing and one on solving — would be good, though.

Before starting I'd like to see what the other mods/community members think. We may want to partially plan it over here first, as well.

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  • $\begingroup$ Yes I thought the same. I think should be very useful if before we individuate the features for a comparison... $\endgroup$ – G M Oct 31 '13 at 21:45
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I've found this review very interesting I think we should learn a lot from there. Another linked reviews:

Israel Science and Technology for 2D and for 3D

Pharmainfo

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  • $\begingroup$ So including an answer that has "review links" might be of value in the final version of this "big list" $\endgroup$ – bobthechemist Nov 5 '13 at 12:33
  • $\begingroup$ @bobthechemist Yes, maybe even in the body of the question a little list of generic useful link... $\endgroup$ – G M Nov 5 '13 at 13:23
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Avogadro (version 1.1.1)


Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

enter image description here TYPE: 3D advanced molecule editor and visualizer, input generator

PLATFORMS: Linux, MacOX, Windows. LICENSE: GNU General Public License

INFOS ABOUT MOLECULE DRAWN:

molecular weight, IUPAC name, Chemical Formula, Energy (kj/mol),Esteem of dipole moment(D) (?), Number of atoms, numbers  of bonds, bonds length.

GEOMETRY OPTIMIZATION: YES

UFF,GAFF,Ghemical,MMFF94,MMFF94s

OTHER FEATURES:

show electrostatic potential surface, crystallography support, find conformers, add hydrogens from pH value, show dipole direction, show hydrogen bonds, show vibrations animation, show spectra, Python console(linux,windows only).

COMPUTATIONAL INPUT GENERETOR:

Gaussian, GAMESS, GAMESS-UK, MOLPRO, MOPAC, NWChem, Q-Chem, Dalton, Abinit

Allowed file format: See OpenBabel

Allowed file export formats:

  CML(*.cml), GAMESS Input (*.gamin), Gaussian Cartesian Input(*.gau), Gaussian Z-matrix input (*.gzmat), MDL SDfie (*.mol), PDB (.pdb), NWChem Input (*.nw), Sybyl Mol2 (*.mol2), XYZ(*.xyz) 
 


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Now that this question was reactivated (thank you ), I guess it is time for an update.

I personally think it was quite a good idea to make such a list. It was also referred in the more recent and more successful proposal: Resources for learning Chemistry (on meta).

To make this , you can find it as its own answer in Resources for learning Chemistry (on Chemistry.se).

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