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

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0answers
25 views

Software/website for finding the synthesis of one chemical compound from another?

I am looking for software or website to find the way of obtaining one chemical compound by list of known/possible consecutive chemical reactions (synthesis or biosynthesis) from another compound(s). ...
4
votes
3answers
397 views

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.
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3answers
103 views

Bond angles in PDB

people I've been trying to adjust the bond angles in a protein data bank (PDB) file, but I'm a novice when it comes to computing so I would like to ask your assistance. I have a file for metamizole, ...
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2answers
100 views

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 ...
6
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1answer
94 views

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 ...
4
votes
1answer
96 views

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 ...
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1answer
92 views

How do I overlay spectra in an ACD/NMR Processor, version 12.01?

I am having great difficulty getting spectra to overlay (the option doesn't even appear) after setting to new window mode and selecting each spectrum.
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1answer
243 views

Software for predicting chemical reactions

I wondered if it was possible to predict the product(s) of a reaction (or even the equilibrium) based on the reactants and the temperature/pressure. I found an answer to a similar question here: ...
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1answer
167 views

Tools to draw molecular structure (wireframe) along with atom numbering

I am looking for open-source tools which can generate 2d molecular structure from the MOL or SMILES file. Further, it SHOULD number the atoms in the order of occurrence of atoms in the connection ...
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0answers
35 views

How can I get ChemSketch to get N and H atoms closer while still operating in ACS style and without adjusting atom sizes?

A person at wikipedia is getting on my case for creating this image because the N and H symbols are so separated even though this seems to be the default of ChemSketch (one of the softwares that's ...
2
votes
1answer
204 views

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 ...
1
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1answer
141 views

Montecarlo simulation in chemistry

I am trying to learn simulation myself and i have installed matlab in my machine for that purpose. In web i have gone through some of the basics of montecarlo simulation but i am unable to find a ...
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1answer
160 views

How would I write an input Lammps command for continuous change in temperature?

I'm going to study the thermal expansion of graphite. For this goal, I should change the temperature continuously. But I do not know how to code it by Lammps?
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1answer
110 views

Avogadro - How can bonds be hidden and only show atoms?

I am using Avogadro for visualizing some cluster systems. Is there a way to hide the bonds of the system, ie. only showing atoms? Thanks!
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3answers
290 views

Open Source tools to draw a set of 2d molecular graphs from sdf file

I have a sdf file for around 50 small-molecules for which I am doing structure-activity study. I would like to draw 2d graphs of all the molecules such that the image would fit into a single journal ...
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2answers
77 views

Mol file of Morphine

I am using the Morphine mol file and I'm attempting to create a matrix which contains a table of the atoms and how they bond similar to a ball and stick format. In the mol file bond block listed ...
3
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1answer
58 views

Are there computer searches for new theoretical minerals in a similar vein to Folding@Home or SETI@Home?

As a surprise gift to a friend I would like to discover a new theoretical mineral and have it named after them. I have some understanding that not all minerals have been discovered, and some minerals ...
4
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1answer
297 views

Tool that generates electrostatic maps of molecules?

Do you know any tools that generate electrostatic potential 2d maps of the molecules as an image?
0
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0answers
42 views

What's an Effective Software For Writing Out Synthesis Steps? [duplicate]

What's an effective Software For Writing Out Synthesis Steps that Works on Linux?
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1answer
98 views

Software/server for calculation of protonation states of small molecules depending on pH

For docking calculations at different values of pH, I am working with flavonoids and would like to know about any software/server that can prepare ligands depending on the pH. Up to now I read about ...
2
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0answers
335 views

Prediction of solubility (from chemical structure) at different pHs

I would like to know What is the best method for predicting the water solubility (and in other solvents) of a compound given its molecular structure at different pHs. What I know now is based on the ...
2
votes
1answer
165 views

Which Chemical Database Software Are Available?

By chemical database software I mean software with similar functionalities to Instant JChem in that they have a large database of different compounds and have the basic capabilities you, or at least I ...
1
vote
1answer
205 views

Chemical software for solving reactions [closed]

I'm looking for a software which can solve chemical equations. For example something like this (given with result): \begin{align} \ce{CH4 + 2O2 & → CO2 + 2H2O} \\ \ce{C3H6 + HCl & → ...
8
votes
3answers
23k views

How do I type a simple chemical equation in Microsoft Word?

How do I type a simple chemical equation in Microsoft Word? I can do subscripts, but long arrows are harder - they do not align with the text. Also, if I want to show a delta above the arrow for heat, ...
0
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1answer
1k views

Software for chemical reaction simulation [closed]

I wonder, what software packs / environments are available for chemical reaction simulation. The goal is to learn or just rehearse some basic knowledge in chemistry. I suppose there should be some to ...
6
votes
1answer
109 views

What does the ZZE tag in an Chemical Table file refer to?

I have a number of Chemical Table files which include a "M ZZE" tag in the properties block. For example, in Galactobuxin, I have: M ZZE 1 31 23 In ...
8
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0answers
100 views

How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
16
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1answer
601 views

What software is used to generate the PDB molecule of the month images?

What software does the PDB use to generate these "cel-shaded" protein models with outlines around foreground atoms? (Leptin: May 2012 Molecule of the Month by David Goodsell)
6
votes
3answers
120 views

How can I perform structure alignment on an inorganic species?

I'm attempting to perform atomistic optimal structure alignment on an inorganic species. Can anyone point me in the right direction to software or a technique for performing this? There exists a wide ...
7
votes
1answer
143 views

Is the Springborg 6D phase space model used in modern molecular orbital modeling?

In a series of papers in the early 1980s, Michael Springborg explored an interpretation of the Wigner phase space function as an electron density in a six-dimensional $(q,p)$ phase space. He applied ...
2
votes
2answers
217 views

A Chemdrawing software? [closed]

I would like to know about a Chemdrawing sotware for 2-d molecular structures. it should be mainly linux based (but if it supports other OS's then that would be great)
14
votes
3answers
732 views

What software can calculate aqueous solution equilibria?

What software is available out there to calculate the equilibrium in a set of reactions in aqueous solution? In particular, I'm interested in software general enough to simulate things like titration ...