Buttonwood
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3 answers
10 votes
819 views
How can I learn LaTeX?
Accepted answer
15 votes

As a gentle, free (as in free beer and as in free speech) on-line introduction, I would recommend learnlatex.org. At the start, you choose one of currently eight languages (Catalan, German, English, ...

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2 answers
11 votes
2k views
Which image format is best to use in a scientific paper?
12 votes

Complementary to the answer given by Nike Dattani with focus on file format, I would like to draw your attention to how you present the content visually in photos, schemes and diagrams known as ...

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2 answers
17 votes
563 views
What are good tools for visualizing glide planes and screw axes?
11 votes

Jmol/JSmol Did you consider Jmol/JSmol? It is freely available for Windows / Mac / Linux, scriptable, may export what is being displayed in formats relevant to chemistry (e.g., .pdb, .sdf), as image (...

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9 answers
18 votes
8k views
How to master Fortran with minimal effort?
10 votes

Extending the answer by Nike Dattani separately rather than an addition in the text: (2) Practicing, bis: After gaining some familiarity with the language, join a "drill site" like codewars....

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2 answers
7 votes
225 views
RDkit and PySmiles results differ on some SMILES strings
8 votes

Speculating a comparison of the outputs by both programs may help, I let RDKit process to SMILES to yield a representation including the atom indices. Derived from the cookbook, the MWE for the ...

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2 answers
10 votes
126 views
How to convert SMILES to Amino Acids sequence using RDKit
7 votes

Based on your recent comment to want to assemble a protein from scratch, and assuming you want to stick to the naturally occurring $\alpha$-amino acids, I suggest to type the amino acids by their ...

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1 answers
11 votes
105 views
Interpret 2D and 3D data from a PubChem summary of organometallic molecule? Can I "flatten" it when showing on a surface?
7 votes

The brief answer, remodeled from the comments earlier given: See the entries of COD, https://www.crystallography.net/cod/4331895.html, and their #4331896, #7220156, and #7220157 -- all coordinated ...

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5 answers
7 votes
1k views
Suggestions on laptops for matter modeling
6 votes

From your lines I assume you start studying chemistry/physics/materials science, and you want to select a computer for performing such computations as well as writing lab reports. Please correct me ...

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1 answers
9 votes
331 views
Proposing a 2D quasicrystal; what are the necessary and sufficient conditions? (If it looks like a duck and quacks like a duck, or...?)
6 votes

Independent of facing a 3D sample, or one of 2D/2.5D, IUCr's definition applies to both of them when stating «There are two definitions of the notion of quasicrystal. A quasicrystal is an aperiodic ...

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3 answers
5 votes
86 views
How to extract specific frames/model from a multi model pdb file?
6 votes

Do you have access to OpenBabel to run from the terminal? For the purpose of demonstration, the example following is demonstrated on a file listing SMILES strings. However, the concept may be applied ...

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5 answers
10 votes
3k views
Is Ubuntu the best option for DFT calculations?
6 votes

If you want to use quantum chemical programs as packaged for and distributed by your Linux distribution of choice, the long term support (LTS) releases of the Ubuntu familiy are typically good to ...

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7 answers
12 votes
2k views
How do I extract a molecular structure from a CIF file?
5 votes

If the content of the .cif in question is fairly molecule-like, my recommendation are the cod-tools collection by the Crystallography Open Database. These may be obtained directly from their web site;...

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1 answers
6 votes
55 views
How are tertiary protein structures represented in computers?
Accepted answer
5 votes

You don't specify what the algorithms shall do. If represented does not equal to visualization, then a the structures may be stored, transferred and processed via the atomic coordinates of the ...

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1 answers
5 votes
48 views
Change in RDKit's encoding of InChi?
3 votes

Following @Tyberius suggest, I departed from using Jupyter notebook in favor of the CLI. In contrast of the GitHub gist,* the following script is to report InChi and InChiKey about pyridine: #!/bin/...

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4 answers
5 votes
348 views
How to edit the first line of XYZ file?
3 votes

More a comment than an answer, note that e.g., for methane 5 C 0.92745 -0.05402 0.04264 H 2.01965 -0.05402 0.04264 H 0.56338 0.81142 ...

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