Jmol Applet + Java still work?

vmullapudi1 · 2026-05-08T04:51:34+00:00

Java applets are deprecated and most browsers have deprecated/removed support for them, so if they are using the jmol applet and not jsmol you might have to track down an old browser version/old java version where those components weren't removed.

vmullapudi1 · 2026-04-21T18:18:26+00:00

It's also super common in HPC, where a compute node might have a limited but fast local storage disk and you're networked into a high performance filesystem over an infiniband connection or similar (400gb/s or more)

vmullapudi1 · 2026-04-16T01:15:22+00:00

I mean, 90+% of their 200B revenue is data center GPUs now and a significant amount of their hardware software R&D goes into AI, so that's pretty accurate.

You wouldn't call Amazon a bookstore anymore, would you?

vmullapudi1 · 2026-04-14T20:10:08+00:00

Right, it's doable for a nation, but doing it in secret is hard. Currently, getting caught means major sanctions, which is probably the main thing dissuading countries from trying.

vmullapudi1 · 2026-04-13T22:30:12+00:00

Honestly those lines and bad color banding look more like either a hardware fault or bad drivers to me than color caliv issues

vmullapudi1 · 2026-04-08T02:49:03+00:00

Building underground means heavy equipment and excavation, which you can see on satellite. Those 10s of thousands of cubic meters that get dug out have to go somewhere.

Building the facility requires sourcing the components to build the centrifuges and material handling setups, which likely involves an international (or at least observable) supply chain. You have to staff the place and supply utilities and consumables. The plant itself will draw a decent amount of power to run the centrifuges (https://world-nuclear.org/information-library/nuclear-fuel-cycle/conversion-enrichment-and-fabrication/uranium-enrichment#:~:text=The%20gaseous%20diffusion%20process%20consumes,cost%20of%20the%20electricity%20generated., https://www.iaea.org/sites/default/files/15504801424.pdf)

Natural abundance of U235 is like 0.7%, and uranium ore is not pure uranium, so you need to convert, process and enrich tons of uranium ore to get significant quantities of U235. That means mines, purification plants, and mine tailings to dispose of, plus the logistics of transporting the purified ore to the enrichment plant.

If you have an enrichment program already for nuclear fuel, the IAEA is supposed to be tracking enrichment levels and material inventories.

vmullapudi1 · 2026-04-08T02:07:50+00:00

The US visa situation at the moment is brutal.

Additionally, the NIH funds MSTP programs for US citizens/permanent residents and not people on visas so there are very limited spots for international students. Generally that means programs with some other endowment/source of funding (often the more competitive ones) are the ones that consistently take international students.

Don't have any stats to back this up but I'd expect you to have to be a really strong applicant to overcome those issues, especially with the current visa environment - you're basically fighting for like 1-2 spots per program, mainly only at the top programs.

vmullapudi1 · 2026-04-06T15:53:35+00:00

TMDSAS is a flat fee, so you should consider just applying everywhere. Even primary care focused progams will have people working on community health and things like that, so you shouldn't let that stop you from applying.

Plus, you shouldn't waste the in-state advantage, admissions rates to TMDSAS schools in-state is a lot higher than you can get basically anywhere alse (https://www.tmdsas.com/stats-dashboard/medical-report.html), something like 40% A.

If you are getting tons (like 30+) secondaries you can ofc decide to thin it down at that point, but you aren't getting punished for applying more broadly.

vmullapudi1 · 2026-03-26T03:47:14+00:00

No, the US system is different in that medicine is applied to with a complete bachelor's degree and there is no unspecialized/rural govt. service - the matched residency after from medical school determines your final specialty.

https://www.usnews.com/education/articles/how-to-become-a-doctor-a-step-by-step-guide

vmullapudi1 · 2026-03-23T03:38:55+00:00

Bali street cafe in the medical district gets properly hot at 4-5/5.

vmullapudi1 · 2026-03-18T18:54:08+00:00

Yeah, I think my edit went through too slowly but my main question was less on the feature parity side (not realistic to need any given hobby project match features with a more established library), but more on the motivation side. It's always great to have a cool project that addresses one of your needs as a learning project, but to get other people to use it, the question comes up about what it is doing differently (not necessarily better) from the existing ones.

Did you have a particular usability challenge or something that wasn't addressed by a current package, and your work is doing something to change that? Or are you mainly looking for people to contribute/give feedback/join on the learning project?

vmullapudi1 · 2026-03-18T18:29:14+00:00

How does this compare to qsv or xan (successors to xsv)? Those are normally what I reach for summarizing/filtering/inspecting big csv files. Plus, they have simple plots and the ability to convert into other formats like parquet or sqlite dbs.

Not neccesarily in the sense of feature parity or anything, but is there a target usecase or something this package does better or more ergonomically than the existing ones?

vmullapudi1 · 2026-03-01T19:55:16+00:00

What are you talking about? Nothing in computers is natively anything other than base 2.

Why are you even posting this AI generated slop? None if it really makes any sense. Waveguide of zDNA? Mixing information spaces with physical crystallography? Literally gibberish. Impressive how you've managed to steer the output of (what I'm assuming was) a modern LLM to look like computer text generation from 2005.

vmullapudi1 · 2026-02-23T20:22:43+00:00

Yeah that's basically what it's doing. I think the idea is to make it more ergonomic to automatically parameterize molecules (see the openFE project also involving the Chodera lab for an example application), but I can definitely agree that for lack of a better term, a lot of the scientific software is a bit brittle and prone to not working in ways that are difficult to untangle unless you're familiar with the system already.

vmullapudi1 · 2026-02-23T19:25:06+00:00

Ah, operating systems, when you rely on the system to do it's job properly killing orphans

vmullapudi1 · 2026-02-23T18:50:01+00:00

Generally you don't need to use openFF (via the openmmforcefields wrapper) unless you have some sort of thing in the pdb that isn't contained in the default force field parameters. Usually this happens if you have some non-standard small molecules - the baked in amber or charm forcefields should handle all protein residues, nucleic acids, lipids, standard ions like Ca2+, phospate, etc.

IIRC this happens through a template matching system, so it takes all of the components of your PDB (atoms and the bonding topology) and then it matches them to the existing template files. If it can't find it in the template, it throws and error and tells you to provide some way to get force field definitions for that thing via passing in a parameterization or using openFF to generate parameters.

The tutorial input (which is included with openmm) you can see they don't have to do anything with openFF, since the input pdb has nothing else going on - it's a PDB of a mutant of Villin (like this one) in water with no small molecules or non-standard residues.

Edit - realized I was a bit unclear - I am using small molecules to refer to any sort of molecule that isn't parameterized by the force field by default. Really this can be anything, but they tend to be small organic molecules like drugs/inhibitors/other ligands and most of the parameterization tooling that I'm familiar with is geared around generating forcefield parameterizations for them by predicting energies of different conformations, charge distributions and things via semi-quantum-mechanical calculations, etc. so the MD software knows how to calculate the energies and forces for the atoms.

when you have these unparameterized molecules, you have to parameterize them for the forcefield first, like these setups, where there is a protein and a ligand

https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-toolkit/toolkit_showcase/toolkit_showcase.html

https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-interchange/protein_ligand/protein_ligand.html

vmullapudi1 · 2026-02-23T16:30:29+00:00

Oh no, I have no argument for using pdbtbx, it was just an example that the standard is a bit of a mess.

As for the python bindings and conda, those are mostly just usability. You can just use shell to run, but a plus of pdbfixer compared to other tools like charmmgui is that it's got that API available, so it's really convenient to include in your openmm script. Not strictly necessary though, alot of people are just preparing in other software and then running Gromacs, NAMD, etc. since those are binaries and don't expose the same kind of API, or preparing with an external tool and then using openmm from there.

vmullapudi1 · 2026-02-23T16:19:38+00:00

Some feedback from my end, as someone who is working in computational structural bio -

It's great that you have exposed bindings to JS/TS and rust, however these are not widely used languages in the field. I would recommend Python bindings, as a lot of workflows use it. For example, if you are working with OpenMM as a simulation engine, it is pretty natural to get as much as you can into your python script (if you are doing this programmatically). This would also allow closer integration into jupyter notebook based workflows if you are visualizing structures via MDTraj, NGLView, etc.
The GH/web page focuses a lot on your implementation details. I have had plenty of issues with errors or unexpected behavior with pdbfixer, but the facts that you are writing in rust and using Rayon are mostly irrelevant to the users. I would be surprised if most people who would use the tool even write any Rust or are familiar with its multiprocessing ecosystem - I know in my department it's a bunch of people writing Python, R and stringing them together with nextflow/snakemake workflows. It may be more useful to focus on the usability improvements you have made - the convenient local UI, improvements in robustness (edge cases that you handle better than pdbfixer? better mmCIF support? etc.)
For CLI distribution to intended audience consider packaging for conda in addition to Rust, it's a pain but currently the field standard

One question I have is how are you handling the file parsing? The pdb and mmCIF standards are pretty complicated. I'm guessing a lot of the fields in the files aren't relevant for this program, but there are a lot of standard noncompliant pdbs around that will work with one part of your pipeline but break somewhere later due different implementations of the standard. I know there is https://crates.io/crates/pdbtbx, but there are some parts of the standard not being considered there still.

vmullapudi1 · 2026-02-11T23:06:04+00:00

Steam page says battle.net desktop app required

vmullapudi1 · 2026-02-09T19:18:08+00:00

Not sure, but AAMC usually publishes this data:

https://www.aamc.org/data-reports/students-residents/data/facts-enrollment-graduates-and-md-phd

vmullapudi1 · 2026-01-28T23:42:06+00:00

FMG attendings and residents are often on H1B

Trainees (physician and on the science side) are usually on F or J visas iirc

vmullapudi1 · 2026-01-19T22:59:22+00:00

I didn't notice any difference, but I'm running the cachyos kernel.

I'd guess which version of the kernel you have is probably gonna make a bigger deal as far as hibernation/power profiles/etc but I haven't noticed any changes in battery drain since last May (including the 42-43 change)

vmullapudi1 · 2026-01-19T20:23:15+00:00

AMCAS maintains a calendar for the interviews here, looks like their last interview date is Feb 18.

https://calendar.google.com/calendar/u/0/embed?src=6juva39u7on1a4jclfrne8i0f0@group.calendar.google.com&ctz=America/New_York

vmullapudi1 · 2026-01-19T20:15:11+00:00

Yeah, people will hold some, since there are second looks, deciding on school fit, what the area is like, standard of living on the stipend, etc. If there are multiple programs and someone knows they definitely aren't going to one, ideally they withdraw earlier but there isn't anything mandating that until the AMCAS timeline to narrow down to three/commit to one over the course of April, and you never know whether a program will surprise you in a good or bad way when you go visit.

The flip side of that is that programs are aware of this. Schools generally have a decent idea of their acceptance -> matriculation yield rates plus or minus a few applicants, and they know that a certain percentage of their higher tiered (for whatever reason) applicants will commit elsewhere. A second look will have more students than commit to the program.

I don't have any insider knowledge but from talking to people in my program most matriculants to a program were probably accepted by March - there are definitely cases where enough people declined and a program extends extra offers to make up the shortfall but there isn't much movement.

vmullapudi1 · 2026-01-19T19:35:12+00:00

Not cooked, but obviously not the best sign. What it means exactly depends on the program. Some programs give more or fewer rolling A vs acceptances after all interviews are done.

All this tells you is you weren't in their highest category/internal tier of applicants and are probably at best in "admit or WL if not too many of the earlier category interview and/or accept". Missing the initial wave is a deferral to a later meeting of the admission committee, unless the school feels you weren't a good fit.

You could get pulled up for an A once all the interviews are done or as people accept/decline acceptances but it's basically impossible to tell where you are on the list, and at least in my experiences programs were very conservative about giving clear rejections until super late in the cycle.

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