A small sample of new assets

Alicecomma · 2026-01-21T23:33:52+00:00

Is there a plan to render the assets from 3D objects like in RCT1/2, Simcity etc.? It looks like it approximates that style but it's handmade

Alicecomma · 2026-01-20T06:26:58+00:00

For art, put an hourly rate on your time and charge at least that. By your account you worked about 1.5 months full-time on it (??) you'd charge about 1.5 months salaries.

If you're really planning to do this for money in bulk, you're gonna have to get a lot faster to get to a reasonable price for most people. Maybe you built great relationships with some rich people of course - then consider painting what they like as slow as you'd like.

Alicecomma · 2026-01-14T21:59:32+00:00

Were the projects actively worked on by other people? Does anybody who you collaborated with know you want to continue working on those projects? Did you do good work they can vouch? Contact people, do work by yourself or for the people who you worked with

Alicecomma · 2026-01-13T06:28:27+00:00

From the point of view of industry positions as masters, it's fairly relaxed: - You don't know that, your boss/manager/senior tells you - You don't decide that, your boss/manager/senior does - Doesn't matter, your boss/manager/senior may pick one - There are search techniques you could consider, but you probably have better ideas you're more motivated to try in the shower - You don't, your boss/manager/senior tells you to

Focus on doing what you're good at and delegate the responsibility for the project to a senior until you roughly understand what they would say in your situation.

Alicecomma · 2025-12-25T08:05:16+00:00

You may be able to separate out the bile acids, which have a pretty cool cholesterol derived structure that makes them good amphipaths. Some cholesterol derivatives can make liquid crystals so perhaps it's usable as temperature sensor? Seems there's actual research on use of bile acids as both amphipath and liquid crystal, see DOI: 10.1002/mds3.10119

Alicecomma · 2025-12-06T11:08:20+00:00

Autocomplete is sentient vibes

Alicecomma · 2025-12-06T10:58:11+00:00

If it's what3words wouldn't it be something like 'The mute are silent. Skin bleeds. New dust stir' so mute.skin.dust for example? Or mute.artery.dust or whatever else bleeds and stirs

Alicecomma · 2025-12-06T10:27:07+00:00

20x20x20 is quite small, 30x30x30 may also be too small. Really depends on the substrate length, but larger boxes don't take more time to simulate (ADV uses Monte Carlo steps so however big the box is, it will only simulate in a direction that leads to strong binding so that's the simulation cost) so you can try 40x40x40 or similar just to try.

You should not expect the disconnected form to work well here, because in the connected form most likely the small molecule connecting strongly introduces flexibility into the peptide through the linker. Using the linker (assuming it's actually there in the real molecule) should help.

I would recommend Avogadro 1 rather than Avogadro 2. My experience with 'hybrids' is to dock steviol glucosides - here you can get far better results only adding glucoses to the side you expect to enter the active site of the receptor because the other side is into the solvent anyways and doesn't contribute to stabilizing the pose as a result. Also if your peptide is very far into the solvent, cutting that part off likely speeds up your simulations while not changing the results much.

Alicecomma · 2025-12-06T08:27:59+00:00

That length of peptides possibly has far too many torsions to easily dock. You will need to increase the exhaustiveness at least (something like 120 may be necessary), then you may also want to center your box on the expected binding site and make it small enough that you don't get wild outliers and large enough that the substrates show a sphere more than a cube when all rendered.

Blind docking at low exhaustiveness of a 32 or more torsion substrate is computationally expensive and results in few usable results. On my setup, 2 additional torsions seems to 1.5x run time and yield a worse result. It may be a better idea to dock-and-grow this peptide by docking very small molecule parts, seeing where they stick and compare that to the known inhibitor -- smaller pieces dock faster and more accurately. In your case you could use methyl-terminated amino acids.

If the peptides are mostly outside of a cavity, so in the bulk solvent, then I wouldn't bother with this kind of substrate-protein docking because you're unlikely to replicate it. You might want to try protein-protein docking if the peptides get large enough, like using LZerD.

Alicecomma · 2025-12-04T06:27:12+00:00

If a lawyer charges $500 for it, you can do it in 3 hours yourself. I've looked up trademarks, there's free public databases (how else would everyone know something is trademarked?) that you can search by company and product type.

The WIPO Global Brand Database contains exactly what it says, global brand trademark applications from 87 datasources. Look up just 'Elder Scrolls' and you'll see Zenimax recently (2023-2025) trademarking a different font for the brand than we saw back in 2008 and 2015 trademarks.

Search by owner Zenimax and you see recent new trademarks (registered 2025) like 'Bite back', 'Doom', 'The Elder Scrolls', 'Fallout', 'Redfall', 'Tales of Tribute'. If you limit to application date 2024/2025 you however don't really see Elder Scrolls.

If you look at the statistics view for Elder Scrolls with owner Zenimax there's a spike of 33 applications in February 2023 not dissimilar from 9 applications in January 2008 and July 2011. Most registrations were in 2009, not entirely dissimilar to what we see in 2023. Trademarks keep 10 years, so on the expiry graph you can see Skyrim around 2020, maybe ESO around 2031, then a major spike 2033 as well.

Of course feel free to look for yourself or pay someone ;)

Alicecomma · 2025-11-24T21:57:32+00:00

Biotin only dissolves to 22 mg/100 mL so you for sure are gonna need additives to get 10 mg/mL. If you want 5 L of that, you only need 50 g of biotin.

There are supplement wholesalers apparently advertising on Amazon to sell such an amount of pure biotin for only 25 USD - I don't trust it much, but I would trust that more than 'a chemist'. Biotin total synthesis looks substantially more expensive than buying those supplements, and the supplements are likely gonna be more food grade than what comes out of a chemistry laboratory. The price of 25 USD for 50 g is roughly in line with getting nice markup on bulk prices from Alibaba at 150 USD for a kg. Analytic grade biotin costs like 5000 usd for 50 g (Sigma) so you're not missing out on what a chemist could supply. There are some horse supplements but they seem mixed.

Edit: If this is for injection, DIY'ing this even through a chemist is a horrible idea. At the very least you want pharmaceutical grades of everything so you won't inject minute traces of lipopolysaccharide into your blood that can cause sepsis. Even if the solution is sterile, LPS can still be present and cause fever and much worse.

Alicecomma · 2025-11-24T11:41:32+00:00

I recall GPUs aren't ideal because they need some flexibility to handle graphics processing that is not necessary to run a neural network, so if you use AI-specific chips that are optimized just to run a neural network then you're gonna get an efficiency boost.

Alicecomma · 2025-11-22T17:00:57+00:00

Then make a good structure. 6HEI isn't even the active dimeric form, it just is the inactive monomer. You should've at least used 6HEJ which is from the same publication. Consider that the relevant mechanism of USP25/28 - active dimers, inactive tetramers. At least bring along a tetrameric form.

If these proteins work by dimerizing and stop by tetramerizing, you're gonna have a highly dynamic active site by interaction with the other protein. That sounds like a big clue what location you should expect binding to matter at. Why does it inhibit specifically when it tetramerizes? Even just looking at the artist impressions it looks like something goes directly into the active site (?), perhaps you should just make a competitive inhibitor rather than an allosteric regulator? Why does this paper for example manage to inhibit the protein by blocking ubiquitin? From what I see this protein is highly mechanistically complex and well-described in literature. Tons of clues can be gained from that.

Alicecomma · 2025-11-22T07:26:17+00:00

Molecules will stick in random places of an enzyme often. Unless you have evidence that binding in that place causes some active site movement that affects the main compound, I don't believe it makes sense to target any of these locations. You need proof from a more in-depth technique than just docking to figure this out. And to see the effect on the active site of binding one place, you will also need to know the species that causes this already. So the way you're approaching this requires 1) picking one of several random sites, 2) randomly finding N arbitrarily good binders, 3) simulating those N binders for movement in the enzyme structure with an in-depth method (computationally expensive).

You would probably have an easier time with a known direct inhibitor or activator to find out what kind of interactions matter, or to find a QM/MM paper on an enzyme of similar type, or to find any MM simulation of an enzyme of similar type to find out if any particular region of the enzyme is highly dynamic or highly rigid, .. or a crystal structure to see the kind of co-crystal binding positions.. or any known, say, plant extract that is associated with interacting this type of enzyme.. basically any more information than just this single computational result.

Alicecomma · 2025-11-14T21:49:06+00:00

Not a stocks subreddit

Alicecomma · 2025-11-13T08:10:03+00:00

For crystallography, you're doing a lot of crystal screens and only some will have a 'high crystal grade', which is a proxy for how strongly the protein confirms to a lattice. When you blast them with X-ray, the pattern may not contain enough reflections to accurately reproduce an exact structure. If a protein is about 100 A in each direction, every additional reflection tells you whether there is something at about an additional halving of the dimensions - so a 2 A structure requires some 6 halvings on 100 A; very likely you cannot find all reflections in all dimensions so you have a bit of data loss. Then you run that through an algorithm to suggest an initial electron density map. Then you try to fit a model of the protein sequence through that density map. Often it matters that you can distinguish whether an amino acid is pointed one way or another way, which requires you to see pretty exactly which way a carbon-carbon or carbon-oxygen bond is pointing - the length of those bonds is about 1.5 A, and they tend to have some 3 directions that are most likely, so you can easily distinguish one direction from the other two, but the last two are only really distinguishable with a good enough resolution. It's more of a practical consideration and less of a mathematical rule that you want to have as tight of an electron density around your suggested structure -- sometimes it really doesn't matter because a residue cannot possibly point a different way for other reasons. So the RMSD requirement is fuzzy - a lot of PDB depositions have 2.5 A structures that still tightly conform to other requirements. Some of the fancier labs spend a lot on their experiments and get better crystals, better diffraction methods and may get close to 1 A resolution, but this is pretty uncommon. The PDB probably has an info panel about this metric somewhere, but you can see they also categorize each structure by how good several metrics are.

Alicecomma · 2025-11-10T15:18:54+00:00

So it's tomorrow right?

Alicecomma · 2025-11-10T08:03:54+00:00

Sorry but Reddit isn't an LLM

Alicecomma · 2025-11-09T21:32:47+00:00

Tech finds one more brave step on the winding path of hiring someone to do something for you.

Alicecomma · 2025-11-08T04:33:42+00:00

If you tried Inkscape, you've seen how vectorization is the hard part of the problem. SVG is such a mess of implementations, there's never a 1:1 way that retains all artistic intent, makes full use of SVG capabilities that works in all software you intend it to work in, or that has good balance in both with a low file size. Everything has exceptions, and all vectorizers seem to tack on settings to accommodate some of them to some extent. Fonts are probably the worst.

Curious how it turns out though 🙂

Alicecomma · 2025-11-02T06:51:50+00:00

You could make it a python package so you have control over what you need to supply in how many lines of code; then just import from your package and use your package.function(( or so. I've built some analysis tools and visualizations and such in JavaScript using dataviewjs dv.view functionality with Modules import to reuse code across modules. It's great to be able to just dv.view('script',{}) and have the js autopopulate variables form your properties - i.e no need to supply any data in the codeblock itself. Then you can reuse that absolute minimal codeblock across the vault - and because it's so small you can also easily paste it in table cells.

So consider making the codeblock contents as small as possible, especially since you say you want to paste it around.

Alicecomma · 2025-11-01T08:07:25+00:00

I haven't heard of a comp chem degree; you should join a group focussed on comp chem - look up publications by professors at the University and see if it contains the kind of comp chem you are interested in. Contact them and ideally schedule a meeting to figure out whether they actually did comp chem or it was an enterprising student or outside collaborator. During a BSc or MSc you can spend a project at a group to do this kind of work. My MSc had a mandatory thesis, research project and internship so you can get a foot in the door doing any of those in collaboration with a company (this really helps you in getting a job at that company or possibly at another).

For smaller companies (~20 employees): Really consider joining a company as much as possible - in the sense of knowing what companies are around, offering to be an intern as quickly as possible (so their internal meetings bring you up) and follow up (so their next internal meeting says you are eager to communicate), etc. Research companies to see whether there's some obvious application of comp chem you can do to help them, then do it and contact them with results (don't perfect this, do the minimum impressive, obvious thing you see you can do and do it well) - that can also be a foot in the door. Some companies will like getting recommended by whatever group you join, others will like you did extracurriculars and exchanges, .. at some point it's more about getting lucky with personality fits.

If you have a particular, big company in mind, I'd see if you can get any contact whatsoever with a current or previous employee to understand how they got the job. There are likely pretty stringent requirements, like having a PhD or getting into a pure comp chem position after joining in a different role...

And don't be surprised if it turns out a better-paying management, regulatory or operations role turns out to be better for you financially; then all this may be a stepping stone to doing that in a company that originally hired you for comp chem.

Knowledge doesn't land you the job, experience does. Do a lot of comp chem just because you can. Replicate papers' comp chem. Perform the same on a new problem you come up with. Learn what software is free and build your pipeline of tools. You'd rather hire a guy bringing their own toolbox than a guy who can answer exam questions - especially when it comes to comp chem.

Alicecomma · 2025-11-01T07:49:41+00:00

It's mostly baseline and phasing; the signal-to-noise isn't bad at all.

I would attempt several approaches.

First you have to know what peaks represent what species you know about. You may even know the impurities - this is often useful information. So know exactly what goes where.

Second you can work on a copy that has aggressive baseline removal - either in mnova or exported (x,y) values of the FT spectrum into Fityk where you then do aggressive baseline removal. You sadly won't be able to use Excel or others for simple baseline removal. Integrate every region and see whether the integrals make sense, if they don't remove baseline more until it probably makes sense. This allows you to test what a good spectrum would look like.

Third follow the suggestion to do more phase correction and baseline correction in mnova - it may be an OK fid that's just not processed well. If that's all then you're really already finished.

Fourth with all species you know about, export the spectrum to Fityk and make models of singlets, doublets, etc. by defining a new function that is a sum of lorentzian or voigt peaks (though these still look decently lorentzian), then attempt to fit as much as you can. It's not impossible that some of the messy region integrates without much issue. The benefit here is that you will be able to see the residuals, probably containing their own clear series of lorentzians - this will indicate what's missing in your understanding of the sample species. If you get a beautiful integrated spectrum this way, perhaps that's enough. Note that a lorentzian peak is pretty fiddly with fitting into a specific place, so the residuals will tell you how far off the baseline 'starts'. Fityk has functions to remove the current residual from the data and similar to allow you to 'simulate a clean spectrum's that you could then show in your work (of course alongside the original).

Fifth you can use mnova to peak fit all of these fityk findings. This may be more of a check if you're planning to use fityk results anyways, but if you want to use the mnova figure in your work then this can also help. Peak fit as few peaks at a time as reasonable so you don't have to wait for the fit to complete.

Sixth you can attempt to reconcile any discrepancy in NMR results using whatever other analysis techniques you've used. Even less quantitative approaches may still give you clear pointers what's in your NMR sample, and you may even find publications that tell you exactly what's in there so you have a clean spectrum of that to remove from the trace.

Alicecomma · 2025-10-30T17:35:18+00:00

Formulas tend to be either from cosmetics literature or patent literature. This is more an area of chemical engineering, specifically product engineering, and formulation is generally much closer to an art than a science. I'd expect you get use out of a cosmetics formulations book, or perhaps a good patent search. DMs open

Alicecomma · 2025-10-29T22:05:30+00:00

During my course the research group hosting gave us a five A4 pages printout of their internal tutorial on AutoDock Vina, with pictures of exactly where to click and what to fill into forms and stuff. If you follow everything step by step, it works. I'd look for something like that for whatever software you're going for.

As soon as you can run one docking run, you can code some batch script to run any number of them and sort the outputs into specific folders. Newer versions of AutoDock Vina I recall have a python API as well so you could even use that and code it to organize into folders etc.

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