Science Answers: Cellular and Molecular Biology Proteins, Lipids, DNA, RNA, etc.


#1

I posted a Protein Data Bank (PDB) import plugin on the Post Here Your Plugins section of the resources page last week and it lead to a tangential discussion about molecular biology. I searched the forum for PDB and saw a number of useful discussions, but a handful of unnerving ones (thankfully older, some outside of C4D) as well where people were jumping through insanely high hoops in efforts to create “molecule-like” blobs. Thankfully guys like Nick Woolridge were already on CG society to help show everyone how easy it could be to import real data.

I want to initiate a clean thread to help answer any questions other members may have about biophysics, biology, structural biology, molecular biology, cellular biology, computational biology, developmental biology, biochemistry, organic chemistry, physics, bioinformatics etc., especially as they pertain to computer graphics (my knowledge gets less reliable as you get further along that list.) If it takes off, I’m hoping we can promote it to the main forum list to help spread the knowledge beyond Cinema 4D users.

In a few weeks, we’ll release a massive plugin that will take care of most biology needs, but in the mean time, I’ll kick this off by pasting over the tangential thread questions and answers that Flingster and I snowballed into over in the plugin forum and hope I can help with any future questions.
Cheers,
Graham


#2

Dear CGtalk Science thread readers,
I’m patching a few pertinent quotes from a plugin thread tangent that got out of control. It starts with the release of a simple plugin, then gets into a short discussion about some useful biology references and notes.
Cheers,
Graham


#3

Flingster posted an amusing tongue-in-cheek joke, and although I appreciated that he realized Flip’s test protein had more significance than a blobby meatball, it reminded me of a fundamental difficulty or barrier that does exist between scientific imagery and the public, so I used my reply as an opportunity to address this for future readers who may not have chemistry or biology training.


#4

hooking into this thread. Havent read through all he info yet–but we bring in pdbs quite often via chimera (osx) or (windows app whose name escapes me–web lab?)
Chimera usually brings in nice detailed spacefilling models and ribbon structures. Sometimes we’ll metaball ball and stick models.

Looking forward to plugin info as well as discussion.


#5

Flingster asked a great question that I had never really thought about:

Which led to my late night ramble about transgenics (transfer of a gene(s) from one species to another) that may or may not make a geneticist cringe, but I’ll paste it here uncensored:


#6

Hi Joel,
Flingster Flip and Johan suggested on the other thread that you, Nick and I get together to initiate a discussion like this… nice to meet you.

I’ve been teaching import protocols since the late mid 90’s and will be publishing an article about it soon… the program you mention is called Web Lab Viewer and used to be my favorite. It once offered a mac version, but they stopped supporting that before OSx took off, so unless you have an old system that can run Classic and an old copy of that software, its dead. Chimera works great, especially for surface models and volumetric electron density maps, cryo EM, tomography, etc. In recent years, I preferred PyMOL for generating ribbon models (it has a little known VRML exporter) that have the molscript style ribbons with the little beaded edges. I periodically used PMV- although a deep program with a steep learning curve, it offers the most flexibility. The PDB maintains a currently list: List of Molecular Viewers at PDB.org, many of which offer .obj or VRML exporters.

If all goes well, we’ll make these old protocols obsolete in a few weeks.
Thanks for contributing,
Graham


#7

hey…here you are…thanks for moving the discussion over into its own thread…will help us in long run and allow for broader discussion.

glad to see Joel jump on in since i know he has a bit of background to it. :thumbsup:
just got to collar Nick to jump in here now…troyan jlslsls etc etc there are a few on here who have or do medical illustration work

Thanks for the links…some great stuff…if others in this field have some interesting links they’d care to share on this field please tag them in here. :beer:

one of the things remo and jonah mentioned was isosurfacing from fluidtools…so maybe its an area could be used instead of the metaball…its very quick at least…just a thought maybe its an area you could look into yourselves if you’d making more plugins or alternatively speak with remo he might be able to help or add to the discussion.

these guys use c4d btw.
http://www.youtube.com/user/nucleusanimation
http://www.hybridmedicalanimation.com/

oh and welcome to cgtalk :cool:


#8

I have only done a small amount of bio-medical type animation work myself but since it represents three fields that fascinate me (science, design and 3d animation) I’ve been wondering how it might be done better.

From a design standpoint it feels to me that 99% of bio-med graphics are pretty weak. Especially with intracellular processes. Nobody seems to know yet where to draw the line with complexity and clarity. There are at least 4 different way to represent a protein, ball and stick, blobby, ribbons, colored atoms; and all of them make me want to fall asleep! Or they look like meatballs. None of them tell me anything useful about what the hell that that protein does. Making a beautiful rendering or animation of one of those models is really putting lipstick on a pig.

One of the biggest problems is our inability to anthropomorphize these complex systems. Things that happen on a cellular or molecular scale, move and behave so differently from what we humans can relate to. The difficulty of an animator trying to convert these processes into something more sensible is compounded by the fact that there are big gaps in the science that explains it.

I am not smart enough to figure out a better way to present this stuff, but i am intuitive enough to know that it is out there waiting for someone to discover it.


#9

Hi folks,
I’ve posted a movie showing competitive inhibition and quasi suicide-inhibition of mock enzymes using the forces available in Mograph 2 (MoDynamics). It comes with a heinously long description, but for those of you interested in simulating molecules, you may find this a helpful read. I did my best (in a spare 45min that is) to explain the biochemistry in terms of the biophysics in plain-ish english.
http://www.youtube.com/watch?v=DySH4y0Ays4
Its all off the top of my head, so I can’t guarantee that is devoid of error, but either way it should give some useful notions about molecular dynamics and you can start contemplating how such simulations could help visually describe basic principles for things you’ve learned as undergrads, like deriving the Michaelis-Menten equation or constant.
Cheers,
Graham


#10

I received a question via email and thought others could benefit from it:

On Jul 14, 2010, at 3:15 PM, mb wrote:
Hi
How can I find my favourite molecule (i.e. PDB code) over the website pdb.org?
Whenever I type name of a particular molecule in the field of search, I face with a lot of molecule name that I don`t want. How can I reach to the exact name?
Thanks

Graham wrote:
Most popular molecules have dozens of variations, or pieces (fragments) available in the PDB. If you’re looking for something common, I recommend finding it at the Molecule of the Month Page and following the links to it from there:

http://www.pdb.org/pdb/explore/motm.do

Here you can find explanations about about molecules written for broad audiences. There are links to the exact 4 digit code structures used to create each image and there are details about the chemistry. If you need a molecule you can’t find on that page, presumably something led you to it. Either a content expert told you to draw a picture of- say, DNA ligase for example, or you read an article- either of these sources should be able to give you the particular 4digit alphanumeric code you’ll need to get the exact structure from www.pdb.org Entering that code into the search field will take you directly to the structure. On occasion, a structure has been superseded by a “corrected” structure, but searching for the original will take you directly to the new one that the scientists decided would be better to use.
Hope this helps,
Graham


#11

We just submitted our paper on the embedded Python Molecular Viewer.
I’m just keeping this thread alive with a teaser to announce that we’ll be releasing a major plugin to solve all of these issues and more for v11.5 on Mac and v12 on all platforms within a month.
Cheers,
Graham


#12

good stuff…keep us updated on the progress please :thumbsup:


#13

on 11/4/10 at 3:00 Pacific Standard Time, I posted a movie with sound… see link below:
In an effort to keep interested parties frustrated and in suspense, I posted a demonstration of ePMV on my youtube site, but the sound didn’t upload. I’ll try to fix it tomorrow. It introduces/demonstrates our embedded Python Molecular Viewer and will lead into videos that guide users through installation followed by tutorials ranging from basic to sophisticated.
http://www.youtube.com/user/grahamj21…
There are links to html instructions in the youtube description for people eager to get started.
Cheers,
Graham


#14

You got me. First, I thought this is nice but lacks a lot of options. But you are developing this into a mature tool. Keep the good work going.

cheers

celke


#15

Yeah, looks very cool. Nice work, Graham. Interesting thread. I’ll be watching for the release.


#16

Fantastic–looks like it will be a great timesaver! Was hoping for a plugin like this for some time now.


#17

ePMV, the embedded Python Molecular Viewer runs molecular modeling software directly inside of professional 3D animation applications!

Ludovic Autin, did most all of the python coding to get Michel Sanner’s Python Molecular Viewer up and running inside many of your favorite 3D applications. We will now rely on you, the 3D community to help expand development of this open-source project into other applications and to enhance its functionality.

I’ve posted a brief movie on youtube that highlights some of the basic functionality of our new plugin package, ePMV. Some of it will be dry for seasoned C4D users, but I tried to make a movie that would show both scientists who don’t use pro 3D apps and 3D app professionals who don’t use molecular viewer software a glimpse of the basics.

This version of the video has sound:
http://www.youtube.com/user/grahamj21?feature=mhum#p/a/u/0/-qHtp4ehseA

I’m working today and tomorrow to create installation videos and will update everyone once posted.


#18

Hi Celke,
I was banging my head against a rock trying to write my own molecular viewer from scratch. I could do some basic things and released a version that made the metaball clouds, but it was a redundant effort to rebuild a wheel (molecular graphics software) that had already been built >30 years ago and fine tuned ever since. Fortunately I was able to get the attention of a very gifted Python programmer in our lab here at Scripps, Ludovic Autin, who could get most of the elements of a very mature molecular graphics package functioning directly inside of C4D. Since it was all Python based, he could take the same libraries and apply them in Blender and MAYA with minimal wrapping. If you get into this stuff, you’ll slowly learn more about ePMV and PMV as you work through the installation and tutorials. They provide an insane amount of power as well as some really simple basic functionalities.
Cheers,
Graham


#19

Thank you for sharing this


#20

That sounds terrific. So, thank you, Ludovic Autin, and the other guys at Scripps. I’ll give it a try this weekend.

cheers

celke