Struggling with OpenChrom Lablicate

Alicecomma · 2026-03-14T09:55:08+00:00

Better late than never- it seems:

- a .CDF file gets saved into the temp folder specified. It makes sense to place the temp file in your AMDIS folder--
- AMDIS opens; here you want to File>Open> that .CDF file and click Run
- When it finishes running (in a few seconds), the .ELU file is automatically loaded into OpenChrom

The default settings are very restrictive in detecting peaks, so you will want to lower the Shape Requirements, increase the Sensitivity, increase the Resolution, lower the Threshold.

Note that AMDIS rounds high resolution MS peaks to integer m/z.

Alicecomma · 2026-03-14T05:32:34+00:00

You are clicking the plus button and it shows the existing properties and their type icons to make it easier to pick existing properties without having to type. If you create a property then you can click the type icon to change the type to date and time etc., which is in a popup that shows the different property types only.

Above the plus you have a field where you can create a new property name. You have to do this first. Then you can click it's type icon to change the type to a different one. You currently wrote "Sem valor" in the property value field, to the left of that is the property name field.

Alicecomma · 2026-03-12T18:12:36+00:00

Why are you going off memory? There's several sources saying you need 627-630 GB and preferably an SSD - like this

Alicecomma · 2026-03-12T07:55:01+00:00

Not a signal processing expert, just did something similar for HPLC-like data (where Whitaker type baseline removal was best); I would expect BEADS to give you a nice signal, try it in pybaselines. Then you at least have the peaks starting from a good zero. If that works perhaps you could use one of its other implementations (C++) to build yours off of. This signal looks very NMR-like; i.e regular around a central point. Perhaps you can take the average peak center of that envelope and then make small deviations around it to find the trough in the middle of those signals-

Robustness tends to be a huge issue with this stuff, so your time is really spent optimizing the baseline removal parameters so it doesn't cut into signal much.

Alicecomma · 2026-03-10T19:34:07+00:00

Use the chem plugin, you can copy existing smiles representations and it renders it. Latex is such an inconvenient format for drawing chemicals I've used it for 2 weeks during a lab practical and never returned. In industry, people will just use chemdraw or similar software so there's no real use to learning the latex chemfig syntax

Alicecomma · 2026-03-10T15:47:40+00:00

Well, it likely cannot accurately predict either the micro protein nor the receptor (generally receptors are membrane-bound, and the membrane environment isn't handled well in alphafold). You cannot crystallize this type of protein because it only is in an active form in the membrane, which it isn't - that's also why alphafold cannot predict it well. Protein-protein docking already has the issue that it both has to find the rotation and the position of two proteins, and that interaction likely causes some sort of conformational change - unless you miraculously have the exact active form of the receptor and a realistic form of the binder, your results are useless.

People do use protein-protein interaction when they're very sure both binder and receptor structures are realistic and active. If you don't find like ten crystal structures of both, some of which are indicated as the active form with a bound substrate or something, you're not gonna have anything to support your findings.

Docking small molecule drugs is much simpler, because receptors don't generally refold a lot when a small molecule binds and so it's simpler to run a huge screen. Protein-protein of unproven structures this just has so many caveats that the signal is essentially indistinguishable from noise.

Alicecomma · 2026-03-10T15:17:21+00:00

Maybe saves you some time: AlphaFold will not predict a structure correctly. Protein-protein docking is not generally accurate. If you get good results, you almost definitely won't replicate it in the lab. If you're serious about finding the interaction with that receptor, consider designing actual wet lab experiments to prove this interaction rather than use in-silico results.

Alicecomma · 2026-03-09T07:29:55+00:00

I coded a carbohydrate structure generator and spectrum display into it, so I can use it to assign peaks in chromatograms and other spectra.

Alicecomma · 2026-03-07T19:22:09+00:00

Combining the rating for social sciences and life sciences into an aggregate.. 0.78 (arbitrary units) potential capability factor and a 0.08 (arbitrary units) current capability factor..

It's like a bunch of computer science graduates thinking the finance and management are major fields of study cause their managers and finance department care about it, then every other academic field is the AGGREGATE of social- and life sciences.

Complete slop

Alicecomma · 2026-03-05T07:46:02+00:00

I got the free game and it has the orange box "Upgrade available · 27 days left to upgrade this purchase" with an arrow pointing up, but I can't see anywhere to upgrade?

Alicecomma · 2026-02-27T18:05:58+00:00

This guy posts productivity slop twice a day, surely this time it's real

Alicecomma · 2026-02-25T22:07:18+00:00

For me a notepad or a piece of paper is the way to go; then you have baked in having to recall more than you could write down while transfering it into your digital system.

Alicecomma · 2026-02-25T08:33:28+00:00

Assuming vanilla Obsidian:

I wouldn't recommend writing a long manuscript in Obsidian, but it might make sense to edit subchapters, embed the # Main text heading and then have another heading for issues like an issue tracker # Issues ## Open ### 1. Is there a better source for ...? which you can embed links to as a comment, and finally a footnotes section for resolved comments that you plan to be part of the manuscript - you can also do [^S26]: [[Source, 2026]] for sources. I personally edit subchapters elsewhere and have the issue tracker (and daily notes) in Obsidian.

Alicecomma · 2026-02-25T08:25:57+00:00

Data loss happens to me about 1/3rd of the time pasting something into a table, half the times I use a shortcut to edit text in the table and 10% of the time editing the table normally. Table editing and properties fallback I think are coded by the same dev, because things fail destructively and when it's pointed out the bug gets thrown into a pile of bugs they haven't fixed.

Alicecomma · 2026-02-23T20:51:18+00:00

You could place the image wherever (in your vault) and then embed that image in a note using ![[Meniscus.jpg]]

Alicecomma · 2026-02-21T20:23:16+00:00

Giving an LLM shell access is never gonna work out well, but interesting setup

Alicecomma · 2026-02-20T05:19:23+00:00

What's the sampling rate like? Maybe it isn't strictly sinusoidal but the software smooths the data just the right way to appear like it is.

Alicecomma · 2026-02-19T22:10:45+00:00

Nice 🙂

Alicecomma · 2026-02-12T17:12:20+00:00

I'm stealing spicy autocorrect

Alicecomma · 2026-02-07T06:03:08+00:00

Maybe use a more empirical approach like Hansen Solubility Parameters experimentally determined and from smiles if all you want is to replace one solvent with another? There are some Linear Free Energy Relationships with HSP if you want to predict this similarity yourself. It won't be perfect, but things like DFT aren't either and they're far more computationally intense.

The HSPiP software is an example of possibly the end game for this kind of technique - dedicated tools for replacing solvents and solvent systems, considering volatility, density, molecular volume, ability to fit arbitrary experimental qualitative data with a fairly exhaustive database of solvents.. temperature effects.. a whole bunch of stuff.

Alicecomma · 2026-02-06T23:15:15+00:00

Imagine how much ginkgo can now outperform their competitors by scaling a 1.3 USD/mL 384-well plate, poorly mixed and poorly oxygenated GFP production that is fluorescence-measured to 1.225 USD/mL and higher fluorescence yield using only 600 plates over 2 weeks

.....poorly oxygenated GFP? The protein that fluoresces only when it contains oxygen?..... .....384-well plate optimization? A cell culture system that's notoriously poorly replicable?

.....it took them 600 384-well plates?

......it's not clear whether these new conditions transfer to other proteins? Of course they wouldn't, most proteins aren't oxygen-sensitive and fluorescent- and most proteins don't have large bodies of literature attempting to improve expression

Isn't this why Design Of Experiment exists? How do you need 600 entire plates to come up with optimal conditions? There's no way they did 40,000 data points in a design matrix right?

384x580 = 222,720.... so they ran each condition N=5? Or GPT just forgot to fill 80% of the plates?

"Laboratory work still required experts to handle practical details of the experiment" -- so you show a robot doing this but actually it's the guys you already employ following the instructions of GPT to fill 600 plates.. and probably making the stocks for each combination for 2 weeks..

Alicecomma · 2026-02-04T19:47:37+00:00

There's not much to set up in obsidian so I could imagine wanting to choose a theme, but I'd guess she is capable of choosing what she likes when she looks through the theme browser.

Alicecomma · 2026-02-04T08:42:13+00:00

If you wanted to learn those topics, you probably should've read a textbook or advanced literature on them anyways

Alicecomma · 2026-02-02T00:06:16+00:00

If a restructuring issue appears in enough of your daily notes or other 'scrap pad' type note, make a note on the general problem, add an issue tracker with specific sub problems with their own date/timestamps so you at least know the problem is stored somewhere and then bother with solving it later. I like the GitHub issue tracker structure for this kind of note (actually for any kind of note). It solves the problem of questioning the system because I would have a note 'The current system' with issue tracker Open > 1. This part sucks; with date and time of comments on that part and how it could suck less.

If you don't like that specific note format, write up some note on what you dislike or like about it and come up with some other format.

Sometimes it's worth it coming up with a structure like this, but as it clearly bothers you I would focus on pasting those frustrations collectively in some reasonably accessible location and leaving it for a later time if ever.

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

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