Marieke Westendorp

I bet this would feel so good if I was a cell.

GitHub - ma3ke/molly: Read xtc files, fast. Read xtc files, fast. Contribute to ma3ke/molly development by creating an account on GitHub.

Depending on the kind of analysis you're doing, you may be interested in checking out molly. It's a very fast reader and writer for XTC files I created and maintain.

For example, molly can often skip reading solvent through clever buffering. And it has python bindings.

github.com/ma3ke/molly

YouTube video by Marieke Bentopy tutorial walkthrough

I just uploaded a video walkthrough of the tutorial I recorded this morning.

youtu.be/C4LYZokS_t4

I love this video so much...

Building realistic models of cells means fitting proteins, RNA, and metabolites at experimental concentrations inside complex cellular architectures. Here's a movie showing how we pack the cytoplasmic space of the JCVI-Syn3A cell:

Cutaway and close-up views of a Martini coarse-grained whole-cell model of JCVI-syn3A, showing the densely packed cytoplasm with proteins, RNA, metabolites, and chromosome inside a lipid membrane with embedded membrane proteins

Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇

Marieke (@ma3ke@hachyderm.io) Attached: 1 image Over the past couple days I worked on a better logo for an important project of mine, bentopy. In the thread below, you can find the making-off story :)

Here is a fun thread about how the Bentopy logo was created, by the way.

hachyderm.io/@ma3ke/11408...

Bentopy: from simple packing to building cellular models – Martini Force Field Initiative

We have an excellent tutorial that is available at cgmartini.nl/docs/tutoria....

In-depth information can also be found on the wiki for the Bentopy repository: github.com/marrink-lab/....

The bentopy logo, packed with proteins using bentopy!

Bentopy is open source software and can be installed directly through pip.

$ pip install bentopy

github.com/marrink-lab/...

Model of mitochondrial compartments. The assembly of the mitochondrial model based on an experimentally informed membrane structure (white), from an empty structure (left) into a mask representation of the IMS (yellow) and matrix (pink) compartments represented by 3 nm voxels. Structures are packed into their assigned compartments based on the mask. In the last section and the magnified inset, structures are colored by kind: Proteins (green), RNA (dark blue), metabolites (pale blue).

Our paper about Bentopy is now published in Protein Science!

Bentopy makes assembling large-scale MD models accessible and fast.

doi.org/10.1002/pro....

@janstevens.bsky.social, @cg-martini.bsky.social

A snowman made of beads with some snow (ions!) around it. It has a black round hat, eyes, a smile, red buttons, and of course a carrot nose.

And here is a still that does not suffer under the heavy burden of the video compression here.

Instead of a tree, I can offer a snowman! ☃️

Built using bentopy, based on David Naranjo's idea.

The input file can be found here: gist.github.com/ma3ke/723f9c....

Instead of a tree, I can offer a snowman! ☃️

Built using bentopy, based on David Naranjo's idea.

The input file can be found here: gist.github.com/ma3ke/723f9c....

Actual picture of a screen, shows a very early stage, rudimentary molecular structure viewer for plan 9

As is tradition, I’m reinventing computational biochemistry on an obscure operating system

plan9 on a monitor set up on a table with a jigsaw puzzle. In the background is a bookshelf and to the side a big pot of colored pencils

I wish everybody a very cozy computation

Wow these are excellent!!

My phone reflects on a window in the Linnaeusborg overlooking the RUG campus as the sun sets

Woah saw some too, yesterday

It is true though.

Almost put ‘I make computers do things fast’ in my bio but bluesky wouldn’t let me.

A colored pencil and black ink pen drawing of a SARS-CoV-2 virion.

I love VMD 🥹

My spiritual home is over at the fediverse but I will take this opportunity to repost only my best material here.