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Tom Goddard
เข้าร่วมเมื่อ 22 ก.พ. 2012
Molecular movies.
How to color proteins in a cryoEM map with ChimeraX
This shows how to color an electron microscopy map so each protein has a different color using the ChimeraX visualization program. It uses a March 2021 daily build of ChimeraX. Three ways to do the coloring are shown: 1) toolbar button, 2) user interface panel, 3) typed command.
มุมมอง: 9 430
วีดีโอ
How coronaviruses get into cells
มุมมอง 42K4 ปีที่แล้ว
Coronavirus, SARS-CoV-2 virus, covid-19, augmented reality We look at the molecules used by coronaviruses to infect human cells including a human corona virus that causes colds and the SARS and SARS-CoV-2 coronaviruses that cause more serious illness. The presentation uses free ChimeraX virtual reality software developed University of California at San Francisco with support from the National I...
Opioid Molecules Mixed Reality
มุมมอง 1.1K4 ปีที่แล้ว
We take a look at opioid molecules morphine, fentanyl, beta endorphin and naloxone and the mu-opioid receptor using virtual reality. This uses ChimeraX VR software. The mixed reality video was captured using an Intel RealSense depth sensing camera and is described here www.cgl.ucsf.edu/chimerax/data/mixed-reality-nov2019/mrhowto.html
Chagas disease drug molecule
มุมมอง 3338 ปีที่แล้ว
Stereoscopic video of a drug molecule for treating Chagas disease. The drug posaconazole is shown docking to a cytochrome P450 protein called cyp51 an essential enzyme for survival of the Trypanosoma cruzi parasite that causes Chagas disease. Clinical trials in 2014 did not find the drug to be very effective. The docking motion was calculated by Christophe Guilbert of UC San Francisco using his...
Chagas disease drug molecule
มุมมอง 4738 ปีที่แล้ว
360 video of a drug molecule for treating Chagas disease. The drug posaconazole is shown docking to a cytochrome P450 protein called cyp51 an essential enzyme for survival of the Trypanosoma cruzi parasite that causes Chagas disease. Clinical trials in 2014 did not find the drug to be very effective. The docking motion was calculated by Christophe Guilbert of UC San Francisco using his program ...
Chagas disease drug molecule
มุมมอง 3948 ปีที่แล้ว
Stereoscopic 360 video of a drug molecule for treating Chagas disease. The drug posaconazole is shown docking to a cytochrome P450 protein called cyp51 an essential enzyme for survival of the Trypanosoma cruzi parasite that causes Chagas disease. Clinical trials in 2014 did not find the drug to be very effective. The docking motion was calculated by Christophe Guilbert of UC San Francisco using...
Chagas disease drug molecule
มุมมอง 5418 ปีที่แล้ว
Stereoscopic 360 video of a drug molecule for treating Chagas disease. The drug posaconazole is shown docking to a cytochrome P450 protein called cyp51 an essential enzyme for survival of the Trypanosoma cruzi parasite that causes Chagas disease. Clinical trials in 2014 did not find the drug to be very effective. The docking motion was calculated by Christophe Guilbert of UC San Francisco using...
Myosin Thick Filament
มุมมอง 1K10 ปีที่แล้ว
This shows a tarantula muscle filament called a myosin thick filament. The molecular motors on the surface of this filament make muscles contract, driving the motion of all animals. The electron microscope data is from Roger Woodhead and Raul Padron and the animation was made by Tom Goddard at the Resource for Biocomputing, Visualization and Informatics using UCSF Chimera software. There is no ...
The Human Brain: Images to Atoms
มุมมอง 22K10 ปีที่แล้ว
A look at human brain optical and electron microscope images,neurons and a molecular channel that conducts electrical signals in the brain. This is a brief look at raw science data with minimal explanation. This video was created for display in a planetarium dome for the 2014 Biophysical Society Meeting in San Francisco. It shows the front half of the dome with fish-eye projection. It was made ...
HIV RNA with new soundtrack
มุมมอง 47511 ปีที่แล้ว
This is last year's HIV RNA video with a new sound track. The new narration is read by Jim Weiss and new music is by Nine Inch Nails. The purpose was to make make the narration easier to hear and use music under a Creative Commons license. The video is identical to the earlier video except for new credits at the end. Here is the earlier video th-cam.com/video/i- ufO9LYg/w-d-xo.html
Great use of AR!
Does anyone know if you can use ChimeraX with Autodock Vina?
Nice!
incredible work!
rna序列，核酸。
Fascinating!!! I'm star struck to see these images.
con you see a protein structure in some kind of microscope ?
The name "Wuhan virus" is a political term, not scientific used by right wing ideologies with an anti China prejudice. It is an essentially racist and xenophobic term. Too bad the political terminology could over shadow the otherwise amazing visuals .
No ill intent. I made this video in late January of 2020 before the virus had a name and before it became political.
thank you
Amazing! I want more teachers like this!
How did i get here?
" Spike protein" & 5G & Covid PROTECTION th-cam.com/video/kTnHBd4AM60/w-d-xo.html
Glyco protein from calcium carbonate in the air ( google it) causing cytokines response then the immune system fails due to angiotensin2 over representation due to too much toxins in the air. Kidney function dictates immunity and our kidneys are working overtime atm with the dimming.
Excelent!!!
one year later, Delightful!
Very informative. Explains the up-down conformation of the RBD. Would you in the update also explain vaccine strategy such as Moderna using proline substitutions to lock the conformation for better binding. Thanks
So helpful and well explained thank you so much
Yikes-spikes!
Viruses don't have goals, they are not cognizant. They simply exist, and things just happen because of the way they are arranged and the automatic things that happen when they interact with their environment. They dont DO anything. Things just happen.
Gracias roca
Great stuff and nice color zone gui button!
Great work sharing the functionalities of ChimeraX. I have been using the software for almost a year and I learn several things in this short video. Thanks!
Oh! wow! science in 21st century !!!! LOL - I have to watch twice because it reminds me Tom Cruise in Minority Report hahahaha!!!! Thank you , Tom , but for people who watch this , it's better to read intensively about this before watching the molecular mechanism between the spike protein and the ACE2. Thanks again Tom.
When the virus hones in on something it doesn't know whether it is the host receptor or an antibody - they both being immunoglobulins and very similar to each other chemically. If the virus wishes to replicate, it is just a chance it must take.
This is so awesome!! I'm really regretting not entering this field.
oh man this is amazing
OMG this is sooooo sick!!!!
WOOOOOW
too dope Tom!!! You da man!!!!!!!
The reason being is cos the sarscov-2 (covid-19) is a coronavirus and HIV is a retro virus............point to note neither one has a gold standard when testing for it and both use a RT-PCR test for diagnosis which is a complete and utter bag of nonsense.......
I'm looking back at this in astonishment given where things have become much less academic. I originally saw this video early on before just to understand virus before it got so bad.
Hi Tom, enjoyed your video on the spike protein - may I ask, what tech are you using? The VR rig. and how you are videoing yourself with the audience being able to see the structures
Details are linked in the video description. I am using a RealSense D435 depth sensing camera so ChimeraX can blend the models in with the room. I am using a Vive Pro VR headset. Other headsets would work too, but I have a Vive Tracker on the RealSense camera to align the camera view with the models. Here's another example looking at the drug remdesivir www.rbvi.ucsf.edu/chimerax/data/remdesivir-ar-may2020/ and another looking at opioids th-cam.com/video/FCotNi6213w/w-d-xo.html
Ok it’s not the Wuhan Virus. It’s SARS-Cov-2-so that’s an error.
Sorry about that. This video was made in January 2020 before the name SARS-CoV-2 was given to the virus, and I thought referring to the location of the epidemic was more informative than calling it the "novel coronavirus" which was its name at the time. Only later did mentioning Wuhan become highly politicized.
Great video. Thank you
Great job.
For a paper on the structure of the coronavirus spike and ACE2, see the following reference: www.nature.com/articles/s41586-020-2179-y
Thank you for this video. Great explanation!
This is a totally badass video and a good summary of the coronavirus structure. I’d like to see in future videos a depiction of the S2 subunit and the conformational changes that take place in the protein in order to facilitate membrane fusion. I’m also interested to see how you think the virus will adjust to a vaccine and its neutralizing antibodies particularly with regard to changes in the polysaccharides and sugars.
WOOOOOOOOOOWWWWWW
WOW!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
wowwwwwwwwwww
Where could I download a WAREZ version of this wonderful software??
And what is going on with that big microwave hanging from the ceiling? Can it cook a egg?
How did you get those cones on your hands. I would like some too. Also, I like eggs.
need more videos on chimeraX pls...
This is a fantastic and very unique way of communicating these things. For anyone out there who may know, how is it that these proteins or groups of proteins 'know'--I know that's probably the wrong word to use--what to do? For example what is it that signals that one protein in the spike to make that movement.
Wow awsome :)
Great Video.Thank you! I wonder when or why does this specific part of the binding area flips out. What causes this mechanism to get active???
increible, fascinante, gracias por tu trabajo.
This video is full of factual information. Thanks a lot for sharing. Stay safe.