toddm

Us old UNIX guys would likely go for cut for this sort of task:

     cut -d " " -f1-2,4-5 file.txt

     one two three four five

     one two four five

Lots of them.

I wrote 6 on my way to my Ph.D. in the late 1990s, and there was plenty of prior art at that time.

Here's one of mine, see references therein as well: https://pubs.aip.org/aip/jcp/article-abstract/110/7/3326/475...

!

Frank Zappa notably said that "nobody looks good wearing brown lipstick."

Except, of course, Silicon Valley, which was before his time but fully predicted in his music as early as 1978.

I can only hope Altman and his ilk are footnotes to history as much as FZ remains a headline.

The American Chemical Society (ACS, predominant professional organization for us chemists) does a Molecule of the Week:

https://www.acs.org/molecule-of-the-week.html

This is really cool and fun!

I don't know much about the security issues others have raised, but if you're good enough to make this thing then I deserve to be pwned by you.

Chapeau!

What does deprecation of an upstream file format - still the most widely-used one, by the way - have to do with support of said format by someone else's software? If anything, it illustrates backward compatibility. And it has nothing to do with a web page describing the use of LEaP. Your comment is simply not germane.

LEaP supports the mol2 format as illustrated in the OP's link, which is substantially better than the PDB format; but again, this thread has nothing to do with file formats and everything to do with the functionality of LEaP.

Finally, it's "deprecated," not "depreciated."

Great to see LEaP (and AMBER) on the front page of HN!

Note that LEaP is one part of the AmberTools suite of programs and is used to prepare systems for subsequent molecular dynamics simulations.

- Long-time AMBER disciple/user

Irrespective of other comments, please do support eBird and Merlin, both freely available from the Cornell Lab of Ornithology (CLO).

I am not associated with the CLO other than as a supporter; they do great work and birders come in as many varieties as birds, including me. The flow of data to organizations such as the CLO is critical and these glasses might help augment that.

The data gathering aspect and mapping bird migratory patterns, populations, and other information from AI-enabled field glasses (as well as the apps and other, as there is image recognition in the aforementioned apps and probably many more I'm not aware of) would be quite helpful for a better understanding of how environmental change affects animal populations.

Take it into the woods and shoot at tin cans and watermelons.

Kudos to Victor for assembling such a wonderful resource!

While I am not acquainted with him personally, I did my doctoral work at UT Austin the the 1990's and had the privilege of working with the resources (Cray Y-MP, IBM SP/2 Winterhawk, and mostly on Lonestar, a host name which pointed to a Cray T3E at the time) maintained by TACC (one of my Ph.D. committee members is still on staff!) to complete my work (TACC was called HPCC and/or CHPC if I recall the acronyms correctly).

Back then, it was incumbent on the programmer to parallelize their code (in my case, using MPI on the Cray T3E in the UNICOS environment) and have some understanding of the hardware, if only because the field was still emergent and problems were solved by reading the gray Cray ring-binder and whichever copies of Gropp et al. we had on-hand. That and having a very knowledgeable contact as mentioned above :) of course helped...

The Ten Commandments are now called requirements.txt.

I am a professional chemist (Ph.D.). After a time, one gets a chemical intuition (as I've heard it called). There are just things that you know or you know where to look and how to filter irrelevant information.

All of that depends on your training and experience. I am not particularly strong in the organic department; however, I am quite expert in areas of physical, aqueous, and computational chemistry. I'm also a geochemist, and have significant lab experience in mostly analytical chemistry. Needless to say, I'm a decent programmer, know a bunch of lab stuff, am quote proficient in linear algebra, and so on. Those main and ancillary skills together give me a pretty good idea of what's going on without having to consult any references.

Resources that I use daily: PubChem, ACS journals, my textbooks, visualization tools, and some software if I'm targeting a certain outcome. IUPAC for naming organics (rarely for me).

Also, I answer questions on the Chemistry Stack Exchange site (not so much these days) which requires a decent amount of digging in order to answer coherently.

I'm still holding on to my CRC Standard Mathematical Tables and Abramowitz and Stegun for when they turn the Internet off.

India is the new Texas.

Former HFT quant here.

Thinly-disguised clickbait/advertising.

Reminds me of being pamphleted in the airport in the early 1990s.

You're not going to get traction using Ruby or Perl for a Ph.D. in astrophysics :)

You have to eat the whole meal (inclusive of the shrimp cocktail, salad, baked potato, and dinner roll) without getting up and without throwing up in the allotted hour.

The no-throwing up rule was instituted some time ago because passers-by (mostly long-haul truckers at the time) would essentially dine for free irrespective of whether or not they completed the challenge. You are also on the hook for the $72, which was not the case back in the day.

See https://www.bigtexan.com/72-oz-steak/ for current rules and regulations.

You could be visiting beautiful Palo Duro Canyon State Park, or passing through as others have mentioned.

You could, like I was many years ago, be doing field work at Pantex as part of your Master's thesis.

The people in the Texas Panhandle and Amarillo in particular are, in my experience, just as nice and welcoming as anyone else - present OP excluded, of course.

Required watching for context is The Plutonium Circus: https://www.imdb.com/title/tt0114147/

I published in refereed journals from 1997 until 2006.

I was in academia - the last one, post-academia - and it was (to me) understood that having peer review was at least a gatekeeper for releasing information that might be useful to or otherwise heeded by the public. Maybe.

Are there problems with that? Are the prices exceptionally high, especially for academic libraries (I recall that Tetrahedron Letters was on the order of $25K in 1995 for a subscription at UT-Austin)? Yes.

But I keep coming back to the standards involved with friendly, neutral, or hostile people vetting your work. It's a higher standard to reach than the free market will entertain, but there is a cost. Keep you on your toes.

The staff and editors need to be paid. Reprints - something from my generation, actual hard copies, some of those requiring color and not BW - cost money. It all costs money.

Do the authors get something in return? Yes. We get refereed journal article citations on our CVs, and that's invaluable.

Love the idea, wish there was a meeting in the middle.

On a positive note, you could have been on Amtrak: https://www.nytimes.com/2023/01/11/us/amtrak-delayed-va-fl.h...

Professional bike fit, $175 from a seasoned coach/racer.

I post on LinkedIn, Stack Exchange, and this site using my real name.

The benefit of doing so is that I have to keep myself in check and really think before I write - yes, there are edits and deletions - and overall the effect has been very positive for me.

Being active on the chemistry SE site has actually proven to be of value in getting jobs related to chemistry - at least 3 employers have said it was useful to see some of my answers - so that is also good.

On the negative side? As far as I know, there is only one other person on the planet who shares my first and last name combination (different middle initial, and turns out to be a distant relative) so there might come a day when I have to do some reputation control should someone impersonate me: but that's not something with a lot of upside :)

python package management

Ph.D. in chemistry here.

The stoichiometry which factors into the definition of pH is

    H_{2}O <=> H^{+} + OH^{-}

(1) H^{+}(aq) is not synonymous with H_{3}O^{+}; the former is aqueous solvated proton, the latter is hydronium ion;

(2) Moving on to the so-called "autoionization" reaction, what you mean to say is that water is self-ionizable or, more appropriately, amphoteric, i.e., is can act as an acid (in this sense, a proton donor) or a base (the hydroxide ion);

(3) The pH of 7 is an ideal and is dependent on temperature, ionic strength, and a few other things (including pressure) that do actually move us off the pH point of 7 for a so-called "neutral" solution; and finally

(4) The units are moles per liter; and hydronium vs. proton does make a difference, as proton is one hydrogen and hydronium is 3 hydrogens.

make, dbx, vi, sed, awk, cut, paste, (s)diff, (f/e)grep, comm, sort, col, column, bash, csh, ksh, man, find, cvs, svn, date, f77/xlf, cc/xlc, bcc, TeX, ghostview

In my opinion, you should not be using AI or apps or anything other than a text editor and TeX/LaTeX to advance your skills here.

My suggestion is to assign to yourself a research topic and write a paper just as you would if submitting it to a refereed journal. Pick something you already know about (or know a lot about).

I am biased - I have a strong academic background and published journal articles, meeting abstracts, and the like - but the outline of title, abstract, introduction, methods, results, analysis, and conclusions provides structure and will help guide you through the process. If you want to be surgical about it, include citations and a bibliography.

What happens next? Find a "reviewer" and tell them to red-ink the hell out of your paper. Make the edits and resubmit it until the reviewer is happy. If you can, gently impose on a friend/coworker who in your estimation is a good writer and has better writing skills than you do. This might cost you a few coffees/beers/pizzas but it will be worth it.

I'd be remiss not to mention the quite-excellent Iron Maiden song of the same name, featuring some dialog from the show at the beginning of the song.

Rock on.

Wargames.

Event Horizon - not quite AI, bit a great representation of what's promised by the technology and what's actually delivered.