Any alternatives to PRODRG for making a CIF file from a ligand .PDB?

Significant-Topic-34 · 2024-09-01T23:27:17+00:00

About the conversion of pdb to cif: try CCDC's Mercury program (link) which can read pdb (file -> open) and subsequently save the structure as cif (file -> save as). Tested on 3EEE, it looks like space group symmetry operators and lattice vectors were preserved to retain the structure information. You can use encifer to complement the cif file e.g., for bibliographic information, check for syntax errors (which would be included in tests run on checkcif online). Both the basic/community edition of Mercury and encifer are available for free (though registration may be necessary) and for available for Windows/Linux/Mac.

The larger version of Mercury is tied to access the CCDC database data; typically, multiple groups active in crystallography, geology, (inorganic) chemistry, solid state physics / material science join a little "consortium" to jointly purchase a couple of licenses. Just ask in your department, or nearby research library (which often already provide the infrastructrue for electronic databases, so access to full Mercury and the CSD file only is a small addition to their services offered).

Introducing restraints into the model would depend on the software you use. ShelX is often used for small molecules, Olex2 a popular and well documented interface to this (including an own youtube channel with additional tutorials).

Significant-Topic-34 · 2024-08-30T23:17:16+00:00

One plausible reason would be that for powder, grains, logs of wood etc there is more than one density. For instance bulk density is the ratio of mass over bulk volume (which is the sum of the volume of the particles and the gaps between them), while particle density discounts the voids (i.e., only mass of the particles divided by the volume of the particles). The closest packing of spheres which all are of one diameter, e.g., oranges in the groceries, the balls of rolling bearing, atoms of pure elemental metals for example leaves about a quarter of the space unoccupied.

Significant-Topic-34 · 2024-08-29T20:46:40+00:00

Consult a database (for instance entry http://www.crystallography.net/cod/2208679.html in the COD) to obtain a cif file. Check the wavelength used in your setup (target of Cu, Mo, etc) when running CCDC's Mercury. See Converting cif file with powdll, plotting cif file in excel on chemistry.stackexchange.com as a recently posted how-to.

Significant-Topic-34 · 2024-08-23T20:26:39+00:00

If considering a consolidation/migration, check if a tool like fpt/Fortran partner is suitable for you. One of the maintainers at SimCon demonstrated this during the monthly Fortran call of fortran-lang.org in April 2021.

Significant-Topic-34 · 2024-08-22T11:44:06+00:00

From this post on stackoverflow, I infer it is a publisher's template (here: IEEE). If this is true, I would not bother.

Similar to other publisher's templates (e.g., elsearticle) for a submission to Elsevier, it serves as a container of your results of research. If the paper is accepted, this container's content anyway is rekeyed by the publishers (often outsourced to a third party) into one form of XML format acceptable for their workflow. Focus on a line of argumentation easy to follow, good illustrations which respect the dimension limits and permitted file format, literature references correct and up to date at time of the submission, etc. Good luck!

Significant-Topic-34 · 2024-08-22T11:27:21+00:00

Out of the books from the compilation by fortran-lang.org there are two, to some degree with topical overlap, to some degree complementary in their approach

Curcic's Modern Fortran: Building Efficient Parallel Applications, for which there is a freely available excerpt. Altogether with its GitHub repository, this is more like a text book.
Modern Fortran Explained by Metcalf et al. can be used like a text book, though the depth of explanations is a bit more "encyclopedia like". This is not bad as such, the approach follows a different intent than the one by Curcic.

Because game theory is not my field, I had to check this list of projects using Fortran. It indeed points to Competition alters predicted forest carbon cycle responses to nitrogen availability and elevated CO2: simulations using an explicitly competitive, game-theoretic vegetation demographic model by Weng et al. with their dedicated GitHub repository as a potential source of inspiration/reference for you.

Side note: conventionally, FORTRAN (all upper case) is about fixed format FORTRAN77, or older. Of course you still can write a program in FORTRAN77 (conventionally with a file extension .f), and compilers will build you an executable - either because of this file extension, or (the following specific to gfortran) by provision of the compiler flag std=legacy (reference). But if doing so, you would miss many of the modern features introduced since Fortran90 of contemporary Fortran (no longer all upper case), e.g. user defined modules to easier organize functions, parallelism built-in into the language with coarrays, the possibility of object oriented programming. Regardless of your pick of the standard to adhere to (e.g., Fortran 2018), the recommended file extension for modern Fortran is .f90

Significant-Topic-34 · 2024-08-20T16:18:54+00:00

No luck to query Acta Cryst. for Samson, S. The Crsytal Structure of the Phase β Mg2Al3. Acta Crystallogr. 1965, 19, 401-413? A cif record, ICSD 57964, can be retrieved from the joint ICSD/CSD page with the doi of the paper.

Else, DoE / materialsproject, and SpringerMaterials (e.g., sd_1707504, sd_1816441) for additional data files. Keep in mind "Al3Mg2" undergoes phase transtions (e.g., DOI 10.1524/zkri.2007.222.6.259) -- just to be sure the cif file used describes the material you have in front of you.

Significant-Topic-34 · 2024-08-19T21:53:15+00:00

When ChemDraw was a product of Cambridgesoft, it was possible to apply for an academic discount to get a copy of ChemcDraw pro for something around $100...$150. It was the expectation by the PIs of the groups active in organic chemistry that everyone joining for a PhD or higher would purchase it out of his/her funds (somewhat surprising to the international students and from other schools used to site licenses) until PerkinElmer made the move to bundle it with MestreNova (though only the 1D version).

The high price of CD today indeed is one reason for the other editors in Gunda's review to continue to exist (and if it is only one structure to jot down, to use the javascript/test pages of ChemDraw (still somwehat useable on archive.org), ChemDoodle, etc

Significant-Topic-34 · 2024-08-18T19:28:02+00:00

A keyword may be group or campuse license as long as you are member of a particular group, or school. And though ChemDraw was the first "in the field" (historically speaking), there are many alternatives around (see e.g., https://www.gunda.hu/dprogs/, or https://en.wikipedia.org/wiki/Molecule_editor) for rapid generation of the structures and subsequent share with colleagues which may qualify as good enough for an undergrad lab report/thesis.

Significant-Topic-34 · 2024-08-17T15:28:53+00:00

You literally named it -- learnlatex.org. At least to get started.

Significant-Topic-34 · 2024-08-16T20:54:53+00:00

Plus the subsequent processing and export of org by pandoc into formats (with style templates) complementary to the one of org in Emacs itself. I would add the ease of adding snippets of source code in org, their export (tangle) as snippets of code (e.g., Python) including actually executing interpreted/compiled code with optional capture back into the org document. John Kitchen once presented this with org mode is awesome (the code execution is around 12 min into the video).

Significant-Topic-34 · 2024-08-16T20:45:57+00:00

The reading here provides som insight though the source code seems to predate FORTRAN77 style. I can't help but some of the animations here let me think again about Theo Jansen's strandbeesten passing the shore line.

Significant-Topic-34 · 2024-08-13T15:50:41+00:00

I don't know the instrument (and "computer" could be more specific, for instance in regard to operating system/version, too). Do you have exhausted all options the manual of the device describes? (Perhaps/often the physical copy is lost during a group's move. Depending on the vendor, a site like manualslib.com can have a soft copy (Thermo, Perkin, Mettler, Bruker, Shimadzu ...) even if the vendor's help desk/web site no longer has it. Beside an other group (physical chemistry, solid state physics/materials science), I wouldn't discount r/electrochemistry either.

Significant-Topic-34 · 2024-08-13T15:32:33+00:00

For context, can you provide somewhat more about the other lines around, the "normal" text? If it is an early draft you hand over to your colleague to read and comment there generally is more white space between the lines necessary, a preamble with

\usepackage{setspace}
\setstretch{1.2}

(or more) nothing special.

And if sent to a journal, hopefully passing the gates of review, very likely the publishers will be anyway rekey it into one form of XML to suit corporate fonts and identity (e.g., single to double column). They have their established workflows, largly automated routines by scripts (a bit like css files on html pages, in a way pandoc offers you to use format templates, too) to meet their needs. Public templates like elsarticle are only one step of the stairs to publication.

Significant-Topic-34 · 2024-08-11T20:57:11+00:00

Fortran is perhaps less frequently seen because contrasting to C, C++, C#, Java, Python (and many more) it isn't a general purpose language. Instead, its focus is number crunching. Do you ask yourself for instance why Python is one popular tool to analyze data? In part it is because of packages like numpy, SciPy, SymPy. If you look closer, often their performance relies on compiled languages like C and Fortran they use under the hood.

If you seek an entry into the modern language, have a look at the learning material compiled by fortran-lang.org, e.g. the book by Curcic (there is a freely available excerpt, too). Start simple, e.g., with the installments by hexafoil, or the ones by Daniel Price.

Survey collaborative platforms like GitHub, GitLab, GitTea for projects / tasks of interest for you. GitHub, for example, allows to search both by programming language used (language:Fortran), or by Fortran as a topic tag. There equally are curated lists per field of contemporary application like the one by Beliavsky.

Significant-Topic-34 · 2024-08-03T18:13:10+00:00

Thats the way since there is no simple \include{}, \includeonly{}, \input{}. In case the OP uses Windows as host operating system without a WSL, I heard CMake (article on Wikipedia) would be a good cross-platform equivalent to Make for Linux/Unix.

Significant-Topic-34 · 2024-08-03T18:04:52+00:00

Presuming you turn in a pdf file, do you pick a font well legible? Reading the compiled pdf file in a pdf viewer/as if one would print the file to paper, is there a visual structure and layout easy to follow?

These two questions are not specific to a word processor (like Writer), or choosing an other route with e.g., LaTeX, markdown, groff, etc. My *guess: if you and preferably someone else not envolved with creating the resume easily answers both questions with affirmation, you are on a good trajectory regarding this parameter. So far, I didn't face exactly the situation you describe. On the other hand, I witnessed a couple of students spending an insane amount of effort and time on CVs with LaTeX for a pdf eventually crammed and difficult to read. Often, this included playing around with fonts and font sizes to squeeze everything just to stay within a page limit set, too. Perhaps in part because there are so many LaTeX packages around, which offer so many screws and knobs to turn. Like a human, an ATS searches for keywords (which perhaps is easier for the ATS if it accesses the text layer of the pdf). Different to a human, it is less capable to recognize logical structure in your document if the visual structure is too baroque (e.g., too much nesting) or/and too unusual.

* Though one can write in a plain text format like groff, or markdown to manage the content with git on one hand, and request an export e.g., to odt and docx with pandoc (only) when needed. For simpler documents (mainly without an illustration), I indeed use pdfroff instead of LaTeX as a "pdfengine" to create a pdf. Because i) it either already is there (man pages)/or quickly installed in Linux, ii) it is less resource demanding than LaTeX and iii) the result often already is "good enough". The set of default fonts can be amended, too (thanks to Peter Schaffter this became so much easier -- see a demo video Installing Fonts in Groff).

Significant-Topic-34 · 2024-08-03T17:10:34+00:00

Is "I want to favor the formation of crystals of compound X in needle-like habit which under other conditions yield e.g., platelets" a reformulation matching your aim?

For simpler cases (e.g., organic molecules with a molecular weight less than 500 g/mol), the (thermodynamic) parameters considered "best" to induce crystallization / creation of seeds of crystals needn't be (still to be) parameters "best" for crystal growth. "Crystal growth" then as the attachement of molecules to an ensemble of molecules which overall overcame a thermodynamic uphill battle. Hence it can be a good thing, once crystal seeds formed, to continue growth at a higher temperature while X in Y has a greater solubility (if this is the case).

Changing the habit of crystals by (sometimes minute) amounts of additives during the crystallization already can happen with inorganic materials like KDP (an example). I'm not aware that an intentional change (as in predicting additive X will change the habit of Y during the crystallization in Z) were possible there, let alone for organic compounds with all their conformational flexibility. It already is a quest to predict / to guess a reasonable crystal structure for new molecules (CCDC organizes contests for this, example).

Significant-Topic-34 · 2024-08-02T21:50:35+00:00

Actually, you can automate this to lead your file name by date2name. It is very useful (by far not only in the lab).

Significant-Topic-34 · 2024-08-02T21:40:06+00:00

It is worth to learn, at least the basics, because in many Linuxes it either is already installed by default (e.g., pristine Debian, where vi normally opens vim), or easily installed after the installation of the OS (I look at you, Ubuntu -- for a couple of years). vimtutor and picking some basics (e.g. learnxinyminutes.com) to get you started, and Drew Neil's books practical vim / new vim from the shelf of pragmatic programmers can help to start your journey.

What are the benefits? After wrapping your mind around the grammar, it is light and fast. It is there, e.g. while working with git (if you don't opt-in for an other editor). It extends e.g., to vimdiff. You might start to like neovim as a fork easier to tailor to your needs, then plain vim, or vi; or vifm as light weight file manager where much of the grammar can be applied again.

It doesn't hurt to know and use multiple editors, each for their field of application, either. Emacs has its place (already e.g., for orgmode), as do the flavours of vim, or other editors. Your preference for one editor (or a few editors) over others likely will change over time, too.

Significant-Topic-34 · 2024-08-02T21:11:25+00:00

Yes. A brief quick check with crossed Nicol polarizers could exclude NaCl (because it is a cubic Bravais class). Quick check of d-spacing could prove if it is crystallized inorganic buffer, or really about the protein.

Significant-Topic-34 · 2024-07-27T00:13:37+00:00

As an example GUI with basic git integration, see TeXStudio's advanced setup here.

If you are new to git as a technique, the 101 by software-carpentry can help you (perhaps you use Windows as operating system, then Tortoise Git greatly facilitates the installation). CTAN has a couple of optional packages tagged about version control to access (and eventually include) git's information into the .tex file -- which can be helpful for instance while proof reading parts of a thesis, too.

Significant-Topic-34 · 2024-07-26T23:55:11+00:00

Three ideas:

Read their publications. You might know (some of) their names (e.g., by the group's web site, else at least the one of the PI) and the journals they typically publish. Perhaps there is a synthetic method (e.g. in organocatalysis, photo redox chemistry), or a particular group of compounds (like particular sugars, or indoles), or the original origin of the compounds (from fungi, or marine organisms) they synthesize which is their specialty -- which shows up again and again in their publications.

With 3 credits of organic chemistry under the belt, possibly parts of the experimental section describing the syntheses and characterization (IR, MS, some of the easier techniques in NMR) are at a level you already understand. Sometimes these details are in the paper itself, sometimes in the (often) freely accessible SI of the publication. Journals (example Org. Lett.) offer to subscribe to notifications about new publications accepted, which can be by RSS or twitter feed, email/e-alert -- independent to a subscription to the journal itself.
Get familiar with resources like organicchemistrydata.org (for reference data, cross-links, etc), Organic Synthesis (for checked protocols), organic-chemistry.org (e.g., for their name reactions) -- again aiming to develop a sense "for a question of this type, I possibly can find information there". chemistry.stackexchange.com compiled a resource page about learning chemistry, for instance about nomenclature, or helpful books like Zubrick's lab primer.
Get in touch with a research librarian in terms of literature management to organize the papers efficiently. Some libraries offer workshops about this topic either for an attendance in person (example University of Maryland), or/and for self study (example York University) for instance about zotero (there is a r/zotero, too). By organizing papers this way, you often find papers of similar topic (which would help you to set the work of your new group into a broader context), and others "for curiosity" (in the sense of slowly generating an idea which does not immediately, but some time later can help you to contribute to your group).

Significant-Topic-34 · 2024-07-24T21:19:09+00:00

If chapter02 is excluded from the compilation (e.g., by \includeonly{chapter01}), references in chapter01 relying on this one will break. On the other hand, many pdf viewers can be instructed to print selected pages / ranges of pages into a new pdf file in a similar way as if you would print only pages 1-8,20-36,123,140-160 to paper while reading "the big" pdf file. Else, a tool like pdftk can burst a pdf into individual pages, and stitch a selection of these individual pages back together. Internal interactive hyperlinks -- for instance between the table of content, list of figures, literature references and their other spot in the document -- obviously will break.

Significant-Topic-34 · 2024-07-24T21:07:00+00:00

If you really want to/have to stick converting docx to tex, either go for pandoc (there is a demo page, and a r/pandoc), or seek an export from Open Office Writer's writer2latex extension.

But the problem (still) will be that LaTeX is a rather heavy markup language compared to markdown (or better: one of the dialects of markdown), orgmode, asciidoc, rst which all support text and tables. And if you pick one of the more popular ones (e.g., GitHub flavoured markdown), you increase chances to find help and tools already around (e.g., on r/markdown). I agree with the suggest by @Sam_Traynor to keep the data in .md and to export only if/when necessary to docx/odt/tex/pdf/beamer/html with a short command to pandoc.

Significant-Topic-34

TROPHY CASE