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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1$\begingroup$ 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 TerrettNov 1, 2013 at 11:34
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$\begingroup$ @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 MNov 1, 2013 at 11:42
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$\begingroup$ @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) $\endgroup$– ManishEarthNov 3, 2013 at 14:17
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$\begingroup$ @ManishEarth - Yeah, I'll give it a go. $\endgroup$– Richard TerrettNov 4, 2013 at 4:32
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2$\begingroup$ @ManishEarth - Just an update - haven't forgotten about this, have a partial list. $\endgroup$– Richard TerrettNov 6, 2013 at 9:09
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$\begingroup$ @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. $\endgroup$– ManishEarthNov 6, 2013 at 9:14
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$\begingroup$ @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 MNov 6, 2013 at 9:18
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$\begingroup$ @ManishEarth Can we write here a list of features post as an answer to this question? $\endgroup$– G MNov 6, 2013 at 9:19
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$\begingroup$ @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. $\endgroup$– ManishEarthNov 6, 2013 at 9:20
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$\begingroup$ @RichardTerrett I've tried design a new template in a new answer... Have you something ready? $\endgroup$– G MApr 2, 2014 at 11:47
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1$\begingroup$ @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 TerrettApr 7, 2014 at 5:54
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$\begingroup$ @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 MApr 7, 2014 at 7:53
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$\begingroup$ @GM Okay I'm working on this right now $\endgroup$– Richard TerrettApr 11, 2014 at 13:27
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$\begingroup$ @RichardTerrett let me know if there is something I can do, I will be in the chat... $\endgroup$– G MApr 11, 2014 at 13:30
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$\begingroup$ I'm for a list, but how do you place it on the site. $\endgroup$– LDC3Apr 20, 2014 at 22:15
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6 Answers
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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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3$\begingroup$ This is good, though I think the array could be replaced by a bulleted list :) $\endgroup$ Jan 9, 2014 at 19:47
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$\begingroup$ 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 ;) $\endgroup$ Jan 11, 2014 at 9:02
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$\begingroup$ @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 MJan 11, 2014 at 9:56
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$\begingroup$ @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. $\endgroup$ Jan 11, 2014 at 10:11
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2$\begingroup$ I made a post on how web based chemdoodle is used chemistry.meta.stackexchange.com/questions/3736/… $\endgroup$ May 23, 2017 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 MNov 1, 2013 at 8:21
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1$\begingroup$ 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 MNov 1, 2013 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.
answered Oct 31, 2013 at 20:41
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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 MOct 31, 2013 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:
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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" $\endgroup$ Nov 5, 2013 at 12:33
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$\begingroup$ @bobthechemist Yes, maybe even in the body of the question a little list of generic useful link... $\endgroup$– G MNov 5, 2013 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.
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 winterbash), 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 status-completed, you can find it as its own answer in Resources for learning Chemistry (on Chemistry.se).
answered Dec 23, 2019 at 0:07