2022 May 24 @ 9:00 a.m. PST: Part 2 of Scientific Visualizations with VFX/science Artist Kate Xagoraris
Part 2 of our Scientific Visualizations series - Toronto-based Kate Xagoraris works at the intersection of visual effects and science. She has created numerous visualizations of complex scientific processes - that are both scientifically accurate and aesthetically compelling. Join this webinar to learn the techniques and tools that Kate uses to create her compelling molecular visualizations.
Download the Houdini Protein Visualization Toolkit referenced in the webinar.
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Webinar Transcript . . .
First and foremost, I want to welcome and thank you for joining us for our GridMarkets Pharma and Media webinars featuring powerful molecular simulation screen and rendering tools. Today's Molecular Visualizations Webinar is the second of our scientific visualization webinar series. Over the next hour we will continue to explore how visual effects artist Kate Xagoraris transforms mode simulation data into stunning visuals animations and scientific models for greater communication impact in today's presentation we will learn how to create cinematic quality visuals from most simulations using the powerful and gold standard of 3d animation software Houdini and grid market services specifically this webinar will include an introduction to Houdini an overview of how to export MOE data into Houdini a description of how to measure and model proteins with Houdini and an overview of our new Houdini protein visualization toolkit which all webinar attendees will have an advanced access to with the links provided at the end of today's presentation my name is Wendy Niemann and I'll be your moderator for our time together today we'll start out with a brief presentation from mark ross with grid markets mark will give us an overview of grid market's molecular simulations screening and rendering services and then we'll hear from our guest speaker Kate Xagoraris VFX artist at MPC Film we'll wrap up with a q a session at the end so please drop your questions in the zoom q a tab located at the bottom right of your screen now without further delay I'm pleased to introduce our first presenter mark ross mark is based in San Francisco and is co-founder of grid markets grid markets offers a secure molecular simulation screening and rendering services which mark will describe in more detail mark thank you for joining us today thank you Wendy I'll keep this very brief a quick overview on grid markets for those of you who are in the pharmaceutical world and maybe computational chemists you can securely run your molecular simulations and screens on the grid markets platform we support MOE amber GROMACS NAMD and quantum bio if you're interested in learning more about that go to our website pharma.gridmarkets.com go ahead Wendy next slide for those of you who are on the media side VFX artist animation studios special effects artists we also run renderings and simulations in our cloud we do that with Houdini which Kate is going to be talking about today but also with a number of other popular 3d solutions like blender Maya 3ds max and Cinema 4d if you're interested in more to learn more on that go to our our gridmarkets.com website and with that Wendy I'll turn it back to you awesome thank you so much mark next up it's my pleasure to introduce Kate Xagoraris VFX artist at MPC Film in Toronto, Canada Kate is an internationally renowned visual effects artist writer professor and industry mentor drawing on her strong bfx background Kate helps researchers and scientists translate their innovative discoveries into stunning visuals to effectively increase the communication impact of their work across a broad range of media she hosts a Houdini user group for VFX artists scientific design and Houdini that encourages outside the box thinking with scientific data and focuses on the beneficial role of visual effects in the scientific visualization and technology worlds in addition Kate runs a VFX site for artists to help them better understand Houdini's scientific visualization value across many research fields including biology quantum materials marine studies and astrophysics over to you Kate hi there okay so let's kind of dive right in and get started I'll start with a brief brief presentation to just kind of bring you into the midst of things first so kind of welcome to our webinar these are this week we'll kind of be breaking down some HDAs that we've kind of developed for Houdini or protein visualization and you're gonna see how you can animate or simulate the data correctly so a little bit more about me I work professionally in the film industry and I've worked on productions such as nightmare alley the Witcher raised by wolves vikings Valhalla and the boys I also run as when he said a popular Vietnamese and science cycle more VFX help and for Katex.com and you can find countless VFX and science related knowledge on there so the focus of today's presentation as we kind of stated we're going to be focusing on proteins ligands creating the in between states for open enclosed models how to visualize various attributes and states the molecule can exist in if we have more time we'll also be breaking down the inner workings of the HDA a HDA today but there are like 19 of them so if we don't get around to it feel free to download toolkit and explore it for yourself uh you might have seen part one of our webinar presentation where we gave an introduction to Houdini and some basic operations that you can do in the software I recommend checking it out if you're new to Houdini and are interested in its inner workings today we're gonna try and waste no time and jump right in as soon as we can but for before we do just some more information on the data sets we'll be working with so we'll be grabbing data from the protein data bank as that works pretty well with Houdini in the demonstration for today we'll be demoing some tools that you can use to read protein data as well as how you can read it successfully if you're wondering where these tools are they're located also on my site and GridMarkets currently good markets currently if you can't locate them and just a quick refresher Houdini refresher for anyone new to Houdini good evening uses something called h these HDAs are also known as OTLs or who you need digital assets they're exactly kind of the same thing just different words in the summary these are subnetworks of various node trees that you can create within the software they're also reusable assets that you can duplicate and share in between builds they also allow for complex scenes to be compressed and make more simplified scenes as well and all of the agas you see here today are custom made to visualize protein data I've tried to make them as physically as accurate as possible and give them a sense of flexibility when you are working with them whether you are an artist or you're a scientist or you work in a scientific field so let's just showcase some of the various HDAs that you can use one of them is the oxyribonucleotide ha and the ribload nucleotide HDA both of them let you visualize and isolate these types of nucleotides in the proteins they count how many there are in the protein they also count the various different elements that contain it that are contained inside the molecule there are color and visualization options and they allow for different visualization options for space filling and wireframe diagram oh let me go back there okay we can also have the chance to visualize amino acids with these tool sets as well so this amino acid HDA visualizes and isolates amino acids in the protein it counts how many they are in the protein it counts the different elements in the protein protein in the specific amino acid as well and it allows for various different visualization options the amino animate HDA you can kind of think of it as an overall animation option that you can apply to your proteins it animates the protein by the temperature factor of the particles we've also created a charge to charge animate HDA as well so you can animate the structure by the overall charge of the atom so we'll keep showcase that a little bit later this has various visualization options as well in color and also if you want to see the average minimum maximum temperature per atom as well so there's a lot of different options when it comes to visualizing the overall animation and temperature there's also something that called the isolate chain HDA and the space filling HDA the isolate chain HDA isolates different chains inside the structure it currently isolates chains a to z so up to 26 different types of possible chains that can exist within your protein it also allows for visual guides to see which chain you are visualizing the space-filling HDA allows for an overall space-filling diagram to be created throughout the structure it allows for different visualizations for the elements again and correct atomic counts within the structure um there's also ribbon and backbone HDAs and virus state h a's I'll skim these through these a little bit quickly the ribbon diagram is a little bit straightforward it allows for ribbon diagrams to be formed within the protein nll and the open in closed state virus HDA or the pirate state HDA only really works with virus proteins but it works with the open and closed states to let you visualize the in-between states of the solve and it works in tandem with the isolate chain HDA if you really want to use it or isolate specific chains there's also the sequencing HDA which allows you to isolate parts of the structure by sequence and also compare the sequences to other proteins so if you have similar proteins you can also just choose pick and choose of which sequences you want to isolate between three of them the atomic property HDA is probably my favorite one because it took the most amount of time to do on a joking side by building this HDA I find finally be thankful towards my grade school chemistry teacher who made this memorize the entire periodic table because this is exactly what this HDA is it's the entire periodic table for Houdini so you can plug it onto a protein and you can see the boiling point melting point charge atomic weight density of all the atoms within the structure and you can also delete any attributes that you don't use the ionization energy HDA calculates the ionization energies per element in the structure and it currently goes and goes up to the first three ionization energy shells per atomic element but that will change in the future and there's color options for visualization we also have various charge field visualization HDAs there are versions of this but I'll get down to that in a second this allows you to visualize the positive and negative charges throughout structure and it creates charge lines to show you where the charges affect each other and how the atoms are scattered throughout the structure as well there's options for using viewing the positive and negative charges separately and trail length options for visualization some of these HDAs might seem familiar because we did cover some of the techniques from our part one presentation however all of them are now new and improved to handle data when it comes to protein structures there's also other hd's available such as the toolkit information HDA which sounds pretty straightforward Van der Waal visualization a residue isolator if you want to see residues left over and structure the electron negativity visualization DNA ribbons if you want to create ribbon structures from DNA structures you can also visualize the bonds inside of structure as well per atom and charge animate as you've kind of discussed earlier in total there are 19 HDAs that you can use for protein visualization in Houdini and these were created over a period of three months this tool set also comes packaged with file examples usable protein data and instructions on how to use it if you were interested we'll also break these down today through the presentation so now we can finally jump into Houdini and sorry if that was a little bit rushed but I want to make sure we can cover all of our content today and I'm really excited to get into it you got a good face Kate you're doing well so now we're going to jump into PDB I want to first show you how you can download data from this in case you haven't already Houdini works best when you go to download files and download PDB format that file format works the best I'm currently working on other HDAs that can handle different other formats so we can get you know import structure fractures and other things but we'll more on that in a different presentation so diving inside here I've kind of created if you're new to Houdini it works for a series of notes so when you first jump into Houdini this section of your network editor is going to be blank until you brought down something called a geometry node and geometry nodes contain allow you to put any nodes that you want inside of them if you want to build a sphere or start to import data for your structure like that but I'm going to jump into a particular node that I've already made for today's presentation that I've given the name of MOE modeling to so we're going to dive in there the first step to importing your data is to drop down something called a file node so the file node basically grabs you can pick and choose your files you can find your file path and you can grab them in I've created myself like a little folder on my desktop where I can just pull in my data from so I have my ligands oriented and my open and close states figured out the more organized you are when you're working with protein data the better often you're going to be working with multiple data sets and it's just going to get confusing so keep yourself organized when you can for this particular tool set when you download it it's going to come in a little folder so a folder called the PDB Houdini tool set I'm going to change the name of the zip file but that's currently what is it as on my desktop the inside of it are three other folders one called do MOE files where you can find this particular file that we've demoed today example data so all the data that we've tested with this tool set is located in here that's also downloaded from PDB and instructions to toolkit content so you can just see the credits of people who helped out on this tool set HDA information instruction instructed instructions a little guide or guide to this stuff and the readme content if you're curious on how this build is progressing so lots and lots of fun stuff in there and then you have your OTL if you want to import these HDAs or OTLs into Houdini there's two ways to do that one you can copy and paste this into your OTL folder when you install Houdini which you go to Houdini OTL and you can import everything into there the other way you can do it is if you go to assets new digital assets you can create new assets that way or you can go to do install asset library and in here you can just pick and choose your asset library of OTL that you'd like to import and then you can just go install install and create from there either way works so now let's kind of get started so I've already I'm working with this particular protein right now and it's called 2pgc and the proteins out of banks so it's this one it's a marine protein so it's not too different from like overall structures if we I'm just dropping down a little transform so I can orient this protein to the center of the world and zucchini I'm not going to go down any go through much hotkeys in Houdini so I recommend like looking that up on your own time if you're new to the software because we'll be focusing on proteins today so I'm going to create some mixed diagrams of this structure so you can kind of see how this looks good how to get started so the first thing I'm going to do is drop down my atomic properties HDA and what this is going to do is going to let me apply all the information that I kind of need to visualize all the different atoms within the structure so if I do color on I can see what type of groups these atoms reside in so currently most of them reside in the nonmetals groups and I can say okay if I if I'm having trouble seeing like the orange color I can change it to red if I really feel like it it's really up to you there's lots of customization there at this stage you can also apply some atomic accurate anatomic sizes if you want to these points I've only included about five at this stage but there will be more and atomic properties if you want to visualize the electron negativity of the structure the density overall density atomic mass and boiling points as well and as well as melting point charges throughout the structure and interval visualization and you might be a little bit weirded out and we go those are not the correct you know density ranges for structure and you'd be right so we're going to use something in Houdini called the geometry spreadsheet and we're going to say okay I'm looking for my density attribute so I can see and of course it's going to not like me so it's very Houdini it gets very particular if you don't capitalize things you just keep that in mind so the maximum density for the structure we're going to say is 4 2 8. and if we just click it again we can see the lowest density of the structure so we're going to go 0 7 2 5 and we're going to click density on so we can visualize that and now we have an accurate I'm going to turn my background to black kind of color representation of how the entire density of each atom is kind of scattered threat structure so moving on to the next HDA I want to demonstrate is something called isolate chain so isolate chain is a little bit confusing visually when you look at it but it makes sense so if we look at this we're looking at change a so chain a if we can switch between them like this chain a chain b chain c like that and we can choose which one we want to particularly look at so I'm going to look at chain a for this particular visualization and I'm going to say I want to create a backbone ribbon diagram from that section I'm going to do that and I'm going to drop that down here and Houdini is going to freak out and it's going to say that wire radius is too small and there we go there's our within diagram and I'm also going to just for fun turn off this text but down here I'm going to say I want to visualize start to visualize amino acids along this chain so I'm going to start looking for my amino acids and now f h e this is now visualized on this ribbon I'm going to merge this back into my structure so we can now use another HDA to kind of visualize maybe some wireframe diagrams scattered throughout it so now you can kind of see the points and the ribbons together I'm going to copy this iso exchange HDA paste it over here and we're going to isolate chain b and now we're going to drop down something called amino acids and we're going to capture start capturing the amino acids of the structure so it's going to say zero because the default amount amino acid this tool set resides on is met so we can start scanning the structure for those amino acids and same like the total element count of all of these is 36. there's four of them right here and there's eight oxygen atoms 20 carbon atoms and eight nitrogen atoms right there and the color to in the words is also corresponding to the colors on the atoms themselves now you might be saying okay this doesn't really work for me I need to process the satellite on after I've isolated this particular amino acid well that's why there's a secondary output of this HDA so we can drop down something called a null in Houdini and now you can just isolate those points right there so if you've wanted to process them later on in a solve of those particular amino acids you could also do that with this HDA and all the information would still be applied to it so the next thing we can say with the structure is say okay I'm going to just turn off my labeling so one way to do that you can go to your amino acids and limit fish this you can turn the color on and off scroll down here and turn off your label I'm going to just keep my color on so it's consistent and go back into my structure down here like backs now I'm going to double check my structure for residues and one day way I can do that is drop down my residue HDA so my residue isolator and I still want to stick around and isolate things on chain b so I'm going to plug that in right here and it's right now defaulting to residue the n but we can start switching between the other residues that might exist in that particular area of the structure and we found one so mse which I think might be overlapping but we'll change the color and see what's going on there let me just check this ah there it is so I'm gonna change the color of this so we can see it better in structure I'm going to say okay I'm going to make these all blue and one day I can the way I can do that is by copying this parameter pasting the relative references into these channels so all of these can also be the same color as well so now we can see this particular residue is located really close to our other amino acids and we can say okay it's right there and there are the atomic counts and other parts structure for this one I'm also going to turn off the labeling now that we know what's there so the another thing we can kind of do with these structures is also create space filling diagrams and diagram so I'm going to isolate another change the chain c and we're going to create a space filling diagram with that as well so I'm going to use my space filling diagram and place it down there we're going to click it and suddenly we have our total atomic count within that space filling diagram we know that this we're figuring I'm this is not chain a so I'm going to turn my chain text off because this face filling diagram has a similar system from the isolate chain HDA built in so you can still isolate parts of the chains but you can also just color code chains in the structure as well and what I mean by color code different chains is that if you plug this into the overall structure you kind of see that now that we've kind of selected chain c we can say I want chain c to be a different color from everything else to highlight it you can do that as well once again you can turn off your account total counts so you can choose what you want to render as well so those are kind of the overall diagram tools and we're going to move on to the next protein so the protein over here I want to kind of showcase some of our other animation tools so I'm once again going to drop down our atomic properties but I'm also going to drop down something called ionization or ionic properties HDA so the ionic properties HDA allow you to once again visualize the ionization energy of the structure so this you might see them i.e. 1 ie2 ie3 so this calculates the first pre-ionization shells of each individual atom in the structure so once again let's say if we just want to look at ie1 we can go to the geometry spreadsheet and we can go i.e. 1 enter and that will find that particular param not parameter attribute for us and we know that the lowest in this particular case is 906.4 and if we scroll to the top it is exactly that number perfect so now we can look at the structure and say okay from blue to red these are these ionization energies in shell one and etc. now I wanted to animate start to try and animate the structure and I'm gonna go to my amino anime tool you can also find your digital assets underneath the digital assets toolbar and Houdini and sometimes that's easier than actually trying to search for them so I'm going to find my amino acid animate and drop that down now everything appears white because it's deleting all the color information from our previous HDA and we can turn on our temperature labels so the suny is going to think a little bit and I'm going to change my background from dark to light and we can go up here and we can say okay um there's a typo error in this this will be fixed as of today but basically it's supposed to list from top to bottom the highest the lowest temperature and the average temperature so it currently just says max but I will fix that as of today it's a really easy fix but we can go down here to our temperature visualizer and start to visualize the hot and cold areas of the structure or which ones have the lowest temperature ranges and which one has the highest so once again we're going to go into here and we're going to say okay I'm going to look for our temperature values and I'm going to delete this and scroll through here which it can be there and find our temperature factor it can start to get a little bit confusing if you have too many attributes on your ad on your structure and we'll showcase how you can start to clean that up after it's snowed so I'm going to also find our lowest temperature factor which is 53.32 and I'm going to look at my structure now and now it's having a more accurate representation of the entire structure as a whole if I turn my background to dark again it's and turn off this annoying grid I can kind of see which structures might have the lowest temperature factor it might be hard to see now that we're streaming but I'm going to try and fix this but I think that some of our DNA strands in there have the lowest temperature factor and we'll visualize those very shortly let me just turn my 0.5 back down three one of Houdini's flexible options is that you can maximize point sizes if you're dealing with points and kind of go through the entire thing that you're visualizing and isolate different things and make them bigger if you have you know if you're seeing impaired or you have difficulty viewing things on your monitor but I'm going to play this back so you can kind of see the overall animation so you can kind of see the hottest areas I'm moving the fastest and the coolest areas aren't really moving at all and so that's what this HDA is designed to do so if you need to add quick and easy animations to your structure this is it there is also another version of this mode called charge animate and we're going to check that out it does the exact same thing but we can visualize the charges of every particular atom as well it might be erroring out because we do not have ah there we go colorature color was not on I don't think there we go and we'll also turn on the labels and I'll change my background to light this one has been fixed so you can see the carbon min max average charge of each atom so I know my probably my range is going to be 5 to negative one probably huh where'd you go man oh it did god disconnected one thing about Houdini that's really fun you disconnect your nodes sometimes things happen so now we can see the overall charge scattered throughout the structure which is pretty cool now I'm going to start visualizing how we can isolate like a big ribbon from DNA and we can drop down isolate chain once again and we can say okay I want to isolate chain a of the structure and now we can have better see the temperature factors in that particular section and if you zoom in right there I think that's our pesky little DNA strand so I'm going to drop down my DNA ribbon and go right there and it might not be in that chain like I thought it would be so we're going to start skimming through this structure so Houdini decides that this is a great idea if that doesn't work you can also say okay that doesn't work you can also just delete this drop this down here and see it right there sometimes if it's connected if a particular like ribbon diagram can only be deformed in one chain dropping down the isolate chain might prevent those connections from occurring so you really have to test the waters to see which HDAs work best with each other but we'll merge these back in so you can kind of see where this is located within our structure so drop this down one really cool thing about this diagram tool is that if you drop down a null you can go right here and you can say okay I only want to isolate that rhythm because let's say I want to animate it later or do something visually really cool with it so I'm going to drop down a carve tool so you can kind of see what I mean by this so if you wanted to let's say animate this over time and make it like very artistic we could do that right here and only work with that online and that this aspect is also implemented in our ribbon diagram tool as well so the next one I think we can use is this one over here and I'm going to start using our charge visualization tools that you can use to kind of better visualize the charges and Van der Waal visualization with structure so I'm once again going to drop down my atomic properties and start to be the base tool that I always use for everything because I need all my element data there and I will drop down my ionic energies just in case I need them and then I can go to charge visualization and let this work and you might already realize that this HDA is a little bit different it has three outputs and these three outputs allow you to isolate the three different things that this HDA will make I'll drop down three different nulls so you can kind of see it so we can do something like this and so the first input over here on the left will allow you to see the full true output of all of this so these are just like the point representations or the geometry built around the points the second input is the points themselves so you can just use color on them and here are our lines as well in case you want to animate them separately so the thing that this one HDA does if we take a look at it we can say oh if we want to animate it we can do it here it has custom anime animate animation options for artists I wanted to also not only keep this accurate but also add artistic elements into these HDAs for artists who want to jump on board this also this little charge thing also shows you visually red to blue which atoms have the lowest range so in this case it's negative three to four so it's showing the charge range from negative three to four just equals charge the highest one we have we can scroll up four and negative three so we're accurately kind of showcasing these positive and negative charges the next thing we can drop down if we go to digital assets is that we can also take a look at Van der Waal visualization which kind of outputs the same thing but this time this visualizes the Van der Waal visualization of the entire structure per atom sometimes in solves you kind of need this information but I also wanted to showcase it visually and new and unique ways for artists too to improve throughout the structure you can also turn these items off so you can see where these lines are emanating from like this and it generates some pretty cool results the next thing I kind of want to go over is if you're working with a structure like we'll jump back over to this one because it's probably the best example of it so let's say I am working with nucleotides and I want to isolate some of them I'm going to drop down this little HDA and I'm going to plug it in I'm also going to pay attention over here and I'm also going to drop down and isolate change HDA and isolate only one part of the structure so I'm going to turn this black so it's dark and we're going to start skimming through to see if there's any nucleotides in the structure if there are it will let us know and we can isolate them and visualize them and if there aren't that's okay that means we can just drop down another tool called assets and this one and now we can do something like this a quick and easy way to search is to drop this and connect it to the overall structure so you don't miss anything as well and this looks pretty clean actually so we might not need it but let's try these on a different structure as well just to make sure that they're working so we will jump over to our first structure and drop this down and I think this one also doesn't have any nucleotides in it either so that's also really great to know and so if I find the the way these tool sets work is that once you have used a certain amount of tools you can say okay in my model there are wireframe models there's backbone ribbon structures there's space filling there's residues and then you can go through each and write down which residue is in structure and then you can try it describe through your image where these are as well so I think presentation wise this is it for Houdini oh yes one more thing we forgot to do MOE is our open and closed state HDA which allows you to visualize solves for virus states and I'm going to drop down my isolate chain HDA so we can isolate the chain of both open and closed states so I have my open open one on the left here and actually let me check my PDB resources sorry my toolbar is a little bit in the way here um we can scroll down and we can see which one it is so I always have these open just in case I need to reference what I'm doing in Houdini and which structures I am working with as well but I'm going to drop down my chain here so you can kind of see what's going on and I want to isolate only chain a for the solve and having them right beside each other once again the transformation node right here is only ice basically just transforming both the the center of world space so we can both have them in the same position for the solve it's nothing too fancy and then we can go virus states and that should appear up here and viruses looks a little bit different and requires two inputs to work and then we can just click that and it should solve the in-between states for chain a of this protein and if there's any movement associated between the same two states and there seems to be a little bit of motion there of between the openness open and closed models you can kind of slightly see it right there it's not too big but if let's say if we were to transform this a little bit up if it wasn't in the perfect position with each other or it wasn't in the center world space you'd probably see a bigger change so it's always important to make sure both of them are in the same area or that might cause issues in your solve and how it might move Houdini is pretty fast at calculating cells but it's always good to be careful that you're solving something correctly so that's another node and once again this has two inputs and outputs the first output being the actual model itself and the second being the wireframe so you can just grab this and animate it further if you feel like it and I think that's the last node that we're going to cover for today so I'm just going to jump back into our 3d presentation as there's some people I'd like to thank for helping build these tools these references and resources and people were very crucial to helping push this in the direction that's going and if you want to use it or test the tool set out please let me know and download it if you have time and I will pass this back off why don't we excuse me get started with questions are you ready for questions Kate yeah cool because we've got one here what are some of the major differences in rendering visualizations in Houdini vs MOE okay so I'm just just brought up that data with me right now so MOE is kind of the I don't want to say it because I don't want to make anybody else use a different you know protein software feel in here but I would consider it like one of the gold standards that you can visualize proteins and it has like a lot of different resources for visual engineering proteins and it's another I don't know if it's but a lot of it's basically used to capture protein data put protein data together salt protein folding and binding and things like that and it's it's used quite wildly by science but the main difference between Houdini and MOE is that MOE was originally designed with the intention only being used for protein visualization as far as I know and it's built with all those function that functions that you could possibly want Houdini on the other hand it was originally designed for the purpose of creating three graphics in multiple industries so Houdini is great in the sense that you can basically build anything you want and you can basically choose if you want to maintain accuracy if you want to go for an artistic approach you can also have presets for materials and multiple render engines as well as complex lighting methods I think Houdini is heading in a huge look dev and lighting route so if you need to have really high so you have something that requires high graphics like lubi's perfect for that and with Houdini there's overall more flexibility when designing your in programming your own tools for visualization MOE’s and like as we talked about MOE has been built also with presets and functions for protein folding at the click of a button but with Houdini it's really up to you of what type of protein salt you would like to program into the software cool all right we have another question Kate they're coming fast and furiously question number two Kate how can Houdini handle accurate animations and representation of protein data and then the follow-on to that how accurate is the software so Houdini is very accurate when it comes to interpreting cells and motions and objects for example some pre-built into the software you know mathematical methods it has for hand delay simulations is it allows you to simulate particle-based and volume-based fluid simulations it also allows for finite element solutions for mathematical modeling and software there's also very various examples in the Houdini community of artists and scientists using huge needs for producing musical sounds using it for visualizing strange tractors spine molds u-heart grafts experiments with delaney triangulation and much more I've even seen recent examples of someone simulate me simulating an electron passing through a spectrum so you can see the energy falloffs and so there's a lot of things that are capable within the software awesome thank you looks like our next question mark is for you the question is how would I get started using grid markets well it's pretty easy on our website there's a free trial button either on the pharmaceutical website which is pharma.gridmarkets.com or the media website which is gridmarkets.com you'll find the free trial button on in both cases go there click on that button and answer a few questions your your name your email address and so on and that will result in a free account and some free grid markets credits will go into your account which will allow you to submit at no risk so there's a there's a step requiring you to download something called envoy that allows you to send your submission to us securely and that's it so steps are basically sign up for an account download and install envoy and then from there you can submit easy peasy sounds super easy thanks mark next question is for Kate Kate in regards to the tools talked about today what are the next steps that will progress them and are there any more protein tools in development so for this toolkit I have a lot of plans I would love the mangle fee to achieve properly showcase protein salts and pve but part of doing that means you have to set up the surrounding data and processes first so my main goal over the past three months has been to do that there's still a lot more I need to do such as the various solves you can calculate for protein folding and motion but that's certainly in development the next plan for these tools will be design where data processing visualization and solving tools some of the tools I would like to achieve in the software are molecule isolation HDAs so something so basically what this entails is like if anything has a water bond within the structure I want to isolate that and showcase it I want to show protein dosing so that's going to be another solver onto itself a degree of freedom HDAs so you can see each degree of freedom of that particular atom and structure or amino acid RNA data sets HDA so basically more functions for bringing in RNA datasets and SVG to Houdini HDAs so we can import import those file formats as well and get that data from it and then further developments of the bonds HDA which we weren't able to showcase today so I want to also showcase the salt bridges and hydrogen bonds as well in between atoms and ring interactions plane atom interactions or playing play things like that awesome hey Kate just I just want to add on the website where you also find the download button for the toolkit there will be a form if anyone has any questions or comments regarding the toolkit or things I'd like to see in it in addition to what you've just said they can put it in that form and or they can use the visualizations at gridmarkets.com email address to notify us of the same one we will be putting that up on a slide in just a moment back to you Wendy thank you that's awesome and looks like we have time for just one more question and that question is for Kate could any other specific excuse me could any other scientific tool sets be developed for Houdini other than protein visualization or is Houdini limited to processing specific data sets so yes shooting is capable of handling different tool sets the best example of this is the Houdini tool set for astrophysical visualization and this is something used by NASA researchers and at various other visualization places downstate it basically processes a bunch of NASA data sets and it's pretty much all python and it works well with scans and VDB data as well so something I'm looking into after this toolkit is how to further visualize quirks and atomic elements in the software so we can visualize spectrums of them and much more and I have been learning leaning into quantum material research a little bit because it's so unknown and there's not a lot of material output of it out there and I would love to make take a stab in the future and figure out how to visualize that science in Houdini and another tool that I am leaning towards is for physically accurate clouds in Houdini as well almost every production I've worked on in the past year has needed some sort of atmospheric rendering so developing a solver and an HDA for those cloud types would save me a lot of time as well make seems more realistic and you could point to a scout cloudscape of Jupiter or something and say that's physically accurate so that will be up my next alley of adventures as well awesome thank you so much Kate that is all the time we have for questions today we'd like to thank our presenters and you our audience for joining us we look forward to seeing you at our next scientific visualization webinar which will take place on Tuesday September the 13th when Kate will be back with us so to save your seat registration can be found on on the upcoming webinar pages of both our grid markets pharma and media websites if you have a scientific visualizations challenge that you would like Kate Xagoraris and who denied to help solve drop us a line at visualizations at gridmarkets.com and we might be able to help visualize that for you during our next webinar in September and also please use that that that email should you have any questions about using the toolkit or suggestions for the toolkit we invite you to stay connected and follow us on our websites and our both media and pharma social channels and again as a thank you for attending today's webinar you all get a sneak peek at the new Houdini protein visualization toolkit at the links on your screen and that were provided in the chat and with that we'd again like to thank you very much for joining us and we look forward to seeing you all in September have an awesome day thank you Kate that was awesome have fun everyone