Biocinematics

Osteocalcin and Bone Mineral

IllustrationStuart JantzenComment

April's Molecule of the Month at the Protein Data Bank features proteins that bind to biominerals. This is osteocalcin binding to calcium ions, a major component of the calcium-phosphate lattice that makes up hydroxyapatite. Hydroxyapatite is essentially "bone mineral", which helps gives bones strength and rigidity.

The glowing spheres are the calcium ions that osteocalcin is currently binding.

The glowing spheres are the calcium ions that osteocalcin is currently binding.

This illustration was the first one where I brought molecular data directly into Houdini, the new 3D application that I have been learning over the past few months. Houdini requires very different workflows from other 3D applications, so learning how to manipulate data for this illustration was interesting and insightful, and I believe processes like this will allow me to create some pretty interesting content in the future.

The green balls here are the important calcium ions. It didn’t take too many nodes to generate this, which is nice.

The green balls here are the important calcium ions. It didn’t take too many nodes to generate this, which is nice.

Houdini can natively read PDB data files like the one I downloaded for osteocalcin, however beyond some helpful data organization, it doesn't have any tools for displaying different molecular representations, so everything from space-filling representations (like the one above) to surface meshes to backbones must be created from scratch. Fortunately Houdini is a great tool for building tools, so I'll be spending some time developing an internal toolkit to show molecules in different visual styles.

A single hydroxyapatite unit: Ca in green, PO4 in yellow/red, and OH in red/white

A single hydroxyapatite unit: Ca in green, PO4 in yellow/red, and OH in red/white

The crystal data for the bone mineral was in a different format (CIF), so I used UCSF Chimera to export a new PDB file and get the measurements that allowed me to expand a single atomic "cell" to the full crystal field of repeated units.

  

Thanks for reading,

Stuart

Backup Strategies

MiscStuart JantzenComment

This Sunday (March 31st, 2019) is World Backup Day! Bet you didn't know that was a thing. Completely independent of that, I thought to share (in the momentary absence of new art) some of my thoughts and strategies for backups. The ideas below are collected from things I have heard and read in conjunction with my own opinions and experiences, and (disclaimer) are not necessarily recommendations for a completely safe and secure system. Implementing any system is never 100% guaranteed; that's unfortunately just an outcome of living in an entropic universe.

Fact: hard drives die. Fact: I am not a data recovery specialist.

Fact: hard drives die. Fact: I am not a data recovery specialist.

What are important features of a complete backup system?

  1. Ability to recover from:

    A) hardware failure (dead hard drive, fried motherboard, lightning strike)

    B) OS/software failure (can't boot into windows, other colossal mess)

    C) malware (viruses)

    D) ransomware (your files are locked until you pay me $₿$)

    E) theft (I'm physically taking your computer out of your physical house)

    F) natural disasters (fire, floods, earthquakes)

  2. Frequent, consistent, verified backups

  3. Fast recovery from common failures

  4. Prevent access by others

  5. Access historical versions (accidentally deleted files, version from last week)

I suppose now is as good a time as any to say, if you don't have any backup at all, please, please do get something. For a "set it and forget it" solution, I recommend Backblaze. It's not perfect or free (it's $6 a month) but probably is one of the best single options to try and fulfill the feature list above. You could instead simply plug in an external drive and copy files to that, but I feel that has three primary weaknesses: (1-CD) a bad ransomware/malware attack could lock up or wipe both, (1-E) it’s easy for someone to steal both your computer and your drive, and (2) it’s easy to be inconsistent and infrequent with a backup schedule. Notice above I said "single option"; a great backup system should have at least two tiers to build redundancy and to fully meet the features listed. You can see how an external drive plus continuous cloud backup (a la Backblaze) starts to strengthen the system because the pros of either part help mitigate the cons of the other. That’s the short version of my thoughts. To dig into the gritty details, read on, brave reader.

What kind of backup system do I use? Before we get there, let's consider the kinds of data I have. First, I have my operating system and programs/software. Yes, I can rebuild from scratch, but that would be a royal pain and a waste of time. I have this data segregated on its own physical drive, the OS drive.

The legendary OS drive

The legendary OS drive

Then I have personal documents, which I don't care to lose, obviously. My photo library is large (30,000+ photos) and is very precious (family photos always are).

Animation projects produce lots of data, easily several gigabytes, while larger projects can produce dozens or hundreds of gigabytes. Some of that is temporary data which can be cleaned out after the project concludes, but while the project is on-going, I do want to keep and protect it.

Finally, there's a lot of ripped media: music and movies (from discs I own, okay?). Fairly easy to recover, so I'm not going to go nuts with the backups, but I don't want to re-rip a ton of CDs and Blu-rays either.

That’s a hefty chunk for one trilogy…

That’s a hefty chunk for one trilogy…

Okay, now I can get to my backup system. My first line of defense is backing up my computer to a two-bay Synology NAS. It's like an external drive that's connected via ethernet instead of USB. And there's two hard drives, so I can fit twice as much stuff, right? Nope: the two hard drives are mirrored (that's called RAID 1), i.e. exact duplicates. This is so if a hard drive fails (it's happened at least twice), all the data is preserved and I just need to stick a new hard drive in to replace the failed one. Side note: RAID is not a backup solution on its own. It doesn't cover scenarios B through F, nor all of A. What and how do I backup to the NAS? I use Macrium Reflect backup software to daily create an image of my OS drive. I have a second daily backup scheduled for all my important data. The NAS isn't huge and I am keeping a few historical backup copies so I can go back in time if needed; this means I have to be a bit selective about the data that's backed up, so some folders (e.g. ripped video) are excluded.

This unit is about 6 years old and has been on almost 100% of that time.

This unit is about 6 years old and has been on almost 100% of that time.

This NAS component does meet several of the features listed. For 1 (recovery), it hits A, B, most of C/D, some of E/F. Number 3 (fast recovery) is a big one. I once had my computer simply not boot. I spent the morning troubleshooting trying to fix the issue. At noon I said forget it and restored an OS drive backup. I was up and running that afternoon. Unfortunately my OS backup was a few months old, which caused more problems than one would think. So now I backup my OS daily. Still, the method works. And for 4 (outside access), no one should be able to gain access to my NAS that wouldn't be able to gain access to my computer. I do wonder how and if I should strengthen that. I don't know quite enough about network security.

Okay, not bad, but we're still screwed in a few scenarios (e.g. fire, massive theft, really bad virus). Also, features 2 (frequent/consistent/verified) and 5 (historical backups) are good here but not great. It's not a perfect "set and forget". Right now it's behaving and verifies all the data, but I've had some hardware/software problems in the past which meant out-of-date or inconsistent backups. Some hands-on maintenance is necessary. And as I said, there's not a ton of space to maintain history. I should get a larger NAS (link to non-existent GoFundMe).

Backblaze working round the clock

Backblaze working round the clock

So I also use Backblaze, which just backs up mostly everything. This covers my ripped media and adds redundancy for the rarer (#1) scenarios I just mentioned. For 2 (frequent/consistent/verified), it's good*, and for 5 (historical backups), you can roll-back anywhere from today to 30 days prior. By default it doesn't backup OS/software, which would likely be hard to restore anyway with this method. If I had to recover from one of the very bad scenarios, a couple days re-installing wouldn't be my worst problem. For 3, recovery time would be slower since they'd have to ship physical drives to me with the amount of data I have. And 4, do I trust them to protect against outside access? It's a good question, and one that prevented me from using cloud backup systems for a long time. The data is encrypted at rest, and I have a strong password and two-factor authentication, but software vulnerabilities and leaks do occur. I suppose in this case I'm on the side of the benefits outweigh risks. Would I rather lose access to my own data or have someone else access my data? I lean toward the former.

Are we done? Well… we could be. But there's that niggle of doubt. What if I have a huge fire and lose my computer and local backups, and then I realize that Backblaze only has two-thirds of my data? Apparently some people have had issues with Backblaze - I can't say for sure one way or the other, but the fact remains that a third-party service can't be trusted 100%*. So for ultimate backup security, I also periodically transfer all my important data to an encrypted hard drive and store it in a safety deposit box at the bank. And… of course you can't just use one hard drive, because the bank vault is empty while you're backing up to the drive. Gotta have two and swap them out. Yep. That should be pretty secure, and meet the criteria for all of 1 (data recovery) and 4 (outside access), and a reasonable rate for 3 (recovery speed). 5 (historical backups) is also good, depending on what I can fit on a single hard drive. The problem is 2 (frequent/consistent): I aim for once a month, but the reality is more like a few times a year. So it's a terrible primary method, but a great tertiary method.

And that's all! Did I miss anything? Do I have a critical vulnerability? Do you have a good system? Let me know in the comments here or on Twitter or Facebook. Happy World Backup Day!

Thanks for reading,

Stuart

 

* Backblaze verification: Backblaze does backup continuously, which means there's typically not much time between making a change to a file and that file being backed up to the cloud. However, verification is something that requires a bit of faith. Apparently all files are checksum’d before upload, but there's no great way to verify that Backblaze has all my data intact. I can check online which files are there, and yes, I can download a random selection of files from time to time, but that's still a random selection of < 0.001% of my files. On the other hand, Backblaze is a successful business employing backup experts, so I'm sure they're doing their due diligence (you had ONE job, right?). Still, at the end of the day, I personally don't like to have one company 100% responsible for my backups, so I don't.

Measles Virus Nucleocapsid

IllustrationStuart JantzenComment

In continuing my illustration series following the Molecule of the Month over at the Protein Data Bank (1), this month I created an image showing the nucleocapsid of the measles virus.

Measles Virus Nucleocapsid - March Molecule of the Month

Measles Virus Nucleocapsid - March Molecule of the Month

I'm sure you've heard of measles before. In fact, it seems to be a bit of an ongoing newsworthy item now and again. Measles is caused by a virus that is extremely contagious and can be deadly (2). Fortunately, we have a widely available vaccine (typically administered together with protection against mumps, rubella, and sometimes varicella (3)) to prevent the spread of this illness.

This image doesn't show the entire virus, instead it focuses on the genetic material (RNA in red) and the protein coat (grey) that protects the viral genes from our bodies' natural defenses (4) and also plays a role in helping the virus make copies of itself through transcription and RNA replication (5).

Making of

I spent a long time looking at the proteins amazingly illustrated by David Goodsell on the RCSB website, and wondering how I might create an illustration of my own. I liked the idea of the long repetitive pattern of the nucleocapsid. When I did some more research, I realized that a long flexible tail was omitted from the structural data (4) and the close-up illustration of the nucleocapsid. Working with my recent method (explained in this YouTube tutorial) I decided to append the flexible tail to the existing data and create something (hopefully) striking. Although the tail originates toward the hollow space in the center of the complex, there is evidence that the tail feeds itself back toward the outside (there's also space limitations with stuffing it all inside), resulting in an external coat of long flexible fibers (6,7).

PDB 4UFT

PDB 4UFT

Once I had that piece in place, it became clear that I could create something quite menacing, using visual inspiration from the Sentinels in The Matrix (which is 20 years old this month!) (8). This approach did have some technical and visual challenges to work out.

A bunch of simulations all stacked up

A bunch of simulations all stacked up

Instead of making 2,516 copies (9) of the nucleoprotein and simulating all of them individually, I decided to simulate a lower number of copies and create static meshes that could be randomly scattered along the length of the nucleocapsid. I figured out the correct transformation offsets I would need to spiral the copies correctly, and used MASH to create a single unit of 37 proteins. Side note: Yes, although I'm learning Houdini, I did use Maya for this illustration because I already know the tools well and I have yet to figure out a pipeline for getting molecular data directly into Houdini.

37 proteins and 222 RNA nucleotides

37 proteins and 222 RNA nucleotides

Then I adjusted the random seed to make several more 37-monomer "units", and sent them over to ZBrush for some retoplogy to reduce the mesh density for all the background units. I also made a lower-resolution RNA spiral unit.

Tip: After retopology of thin meshes, use the 3D Gizmo and ctrl+drag the yellow center to inflate the model closer to the original volume.

Tip: After retopology of thin meshes, use the 3D Gizmo and ctrl+drag the yellow center to inflate the model closer to the original volume.

Turns out the RNA is all cytosine residues… so not perfectly accurate… shhh!

Turns out the RNA is all cytosine residues… so not perfectly accurate… shhh!

 Finally, I used MASH again to spread the units along a curve, and posed the whole assembly to my liking.

I believe this is approximately the correct full length of the measles genome, and yes it should fit inside a typical measles capsid. Successful assembly!

I believe this is approximately the correct full length of the measles genome, and yes it should fit inside a typical measles capsid. Successful assembly!

I feel like the RNA is the most central and dangerous aspect of this virus, so I wanted all of the color in the image to come from that and have it draw the eye. Because of how the protein binds to the RNA, I didn't get as clean a view of the RNA helix as I was hoping, but I think overall the image works as intended. I hope you like it.

No connection to the Xbox Red Ring of Death

No connection to the Xbox Red Ring of Death

Thanks for reading,

Stuart

 

References (fancy!):

  1.  PDB101: Molecule of the Month: Measles Virus Proteins. RCSB: PDB-101 Available at: http://pdb101.rcsb.org/motm/231. (Accessed: 12th March 2019)

  2. Measles. World Health Organization (2018). Available at: https://www.who.int/news-room/fact-sheets/detail/measles. (Accessed: 15th March 2019)

  3. MMR Vaccination | What You Should Know | Measles, Mumps, Rubella | CDC. Centers for Disease Control and Prevention (2018). Available at: https://www.cdc.gov/vaccines/vpd/mmr/public/index.html. (Accessed: 15th March 2019)

  4. Gutsche, I. et al. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid. Science 348, 704–707 (2015).

  5. Jiang, Y., Qin, Y. & Chen, M. Host–Pathogen Interactions in Measles Virus Replication and Anti-Viral Immunity. Viruses 8, (2016).

  6. Jensen, M. R. et al. Intrinsic disorder in measles virus nucleocapsids. Proc. Natl. Acad. Sci. U. S. A. 108, 9839–9844 (2011).

  7. Desfosses, A., Goret, G., Farias Estrozi, L., Ruigrok, R. W. H. & Gutsche, I. Nucleoprotein-RNA Orientation in the Measles Virus Nucleocapsid by Three-Dimensional Electron Microscopy. J. Virol. 85, 1391–1395 (2011).

  8. The Wachowski Brothers. The Matrix. (1999).

  9. Lund, G. A., Tyrrell, D. L., Bradley, R. D. & Scraba, D. G. The molecular length of measles virus RNA and the structural organization of measles nucleocapsids. J. Gen. Virol. 65 ( Pt 9), 1535–1542 (1984).

Maya Tutorial - Making of: eIF4E

TutorialStuart JantzenComment

Today I released a tutorial about how to use Molecular Maya’s Modeling Kit to fill in a missing region from protein data, based on the illustration I shared in my previous post. You can learn more about Molecular Maya and the modeling add-on kit here (https://clarafi.com/tools/mmaya/), but even if you don’t have the kit, there’s still a number of points about structural data and how to understand PDB reports that may be helpful.

The protein up for demonstration here is a eukaryotic translation initiation factor (English: It helps get messenger RNA to the ribosome so proteins can be made). The challenging thing about this protein is it has a long flexible “disordered” tail that is not included in the x-ray crystallography data, because flexible poorly-structured regions just don’t crystallize well, so this is a very typical scenario when trying to use Protein Data Bank (PDB) files.

Fortunately, we do know the amino acid sequence of this tail, and we can use features of the mMaya modeling kit to synthesize and simulate the missing region, allowing us to complete our protein model.

I hope this tutorial is interesting and useful. If you have questions or if you’d like to see a tutorial on another aspect of building molecular models, you can ask me in the YouTube comments, or DM me on Twitter, or any number of ways!

Thanks for reading (and watching)!

Stuart

A Fresh Start

Misc, IllustrationStuart JantzenComment

If you've been following my work for any length of time, you're probably aware that I've kept a blog over at biocinematics.blogspot.com. This week I reached the 10th anniversary of that blog and decided it was a good time to "reboot" the blog fresh and new on this site.

 So here we are!

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Blank Page Syndrome!

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Oh, I'll share the first image from a series of a molecular illustrations I started which is inspired by the Molecule of the Month series created by David Goodsell at the RCSB Protein Data Bank.

Initiation_Factor_eIF4E

The February Molecule of the Month is the eukaryotic initiation factor eIF4E. By binding to the 5' cap of mRNA (seen in the lower part of the image), eIF4E helps bring mRNA and the ribosome together to start protein synthesis. eIF4E also features a disordered flexible "tail" (in the upper left) which is involved in binding other parts of the initiation complex.

If you are on Instagram, I suggest following me @biocinematics to see more of this series as I create more molecular portraits.

On a related note, if you haven't yet seen anything on my "Blog 1.0", and you want to catch up a bit on recent news, I'd encourage you to have a peek at these posts:

10th Anniversary: The end of one blog and the beginning of another (and my demo reel!)

Knots and Robots: Recent client work

And now for something (almost) completely different: Job changes and new beginnings

 

If you want to read some humorous off-topic stuff, I'd recommend these:

Changing a Hard Drive

Bad auto transcription

One thing I would strongly caution against is going right back to 2009 to see the ugly beginnings of learning difficult software. Or… /shrug I can't stop you.

 

Thanks for reading!

Stuart