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Kate Xagoraris


2023 Jan 26 @ 9:00 a.m. PST: Part 3 of Scientific Visualizations with VFX/science Artist Kate Xagoraris

Part 3 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.  Attendees will be provided access to the Houdini Protein Visualization Toolkit.

Download the Houdini Protein Visualization Toolkit referenced in the webinar.

See HERE for our other upcoming webinars.  


Webinar Transcript . . .

Welcome and thank you for joining us for our GridMarkets webinars featuring powerful molecular simulations and Screen tools today's webinar scientific visualization is the third of our scientific visualization series over the next hour we'll explore how visual effects artist Kate Xagoraris transforms molecular simulation data into stunning visuals animations and scientific models for greater communication impact in today's presentation we'll learn how to create cinematic quality visuals from molecular simulations using the powerful gold standard of 3D animation software Houdini and GridMarkets Services specifically this webinar will include an introduction to Houdini an overview of how to export a protein database into Houdini a description of how to measure and model proteins with Houdini and an overview of our new Houdini protein visualization toolkit which will be available on the GridMarkets website the link will be provided at the end of Kate's presentation my name is Wendy Niemann and I'll be your moderator for our time together today first we're going to start with a brief presentation from Mark Ross with GridMarkets Mark will give us an overview of GridMarkets's molecular simulations and screening service and then we'll hear from our guest speaker VFX artist Kate Xagoraris finally 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 and 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 GridMarkets GridMarkets offers secure molecular simulation and screening as a service which Mark will describe in more detail mark thank you so much for joining us today over to you I'm going to give a brief introduction excuse me to who GridMarkets is and before I do that I'd like to thank Kate for being our guest today so thanks very much Kate for joining us today I'm looking forward to the to the webinar with you so gridmark is basically provides two different Services one for our pharmaceutical customers who run molecular simulations and screens we support Amber gromax and AMD and Quantum bio and the second is GridMarkets media which allows Studios animation artists folks like Kate to render and simulate their scenes at scale we support Houdini Maya Cinema 4D blunder and 3ds Max on the media side and you can find us on the media side at so that's pretty much all I wanted to say I'm going to hand it back to you Wendy thank you Mark next up it's my pleasure to introduce VFX artist Kate Xagoraris who's located 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 users 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 UK hi everybody thank you Wendy for the Great lead in there so yes a little bit about me I am going to be a sex artist in Toronto uh some stuff that I've worked on besides scientific visualization our Guillermo del Toro Pinocchio Raised by Wolves and Viking Valhalla today we're out we're going to be revisiting our proteins toolkit for Houdini uh we've been working on this toolkit for over a year now so it's been pretty awesome to see how the progress has developed over the period of a year and so just a little recap for everyone who's just jumping into this presentation just in case you haven't you know seen the previous ones over the past year uh I've been trying to develop tools for side effects Houdini's scientific visualization particularly for protein visualization in the software and it all kind of started out with building basic tools for modeling different types of diagrams such as space filling wireframe and Rhythm diagrams and then tools for modeling residues amino acids and elements of proteins as well as much more uh since then the toolkit has also developed animation options for animating with Browning noise animation through temperature factors charges and risen animation and one of the purposes of doing this was to test the limits and abilities of Houdini as well as make them make tools like this more accessible uh for the software when it comes to Scientific visualization this toolkit is open source and is available to download from my site and GridMarkets and today we will also be doing a quick review of the older tools we have developed in the previous presentation as well um So currently we have more nodes and updates that have been added so this is a little highlight of them all of what we're going to be jumping into today after talking with some people in the scientific illustration and visualization Community they recommend and I make some changes especially to the backbone ribbon diagram node previously this node only showed the backbone of the protein and now it shows the direction of the ribbon and more accurately showcases the spiral shapes of the curve so very very much a big thank you to those people who reached out and gave me that input and today for the new nodes that we'll be talking about uh we have things such as hydrogen bond counts assault Bridges hydropic phobic forces to cover there's something called a nanotube fun HDA that's simply just for artistic modeling with proteins that we can touch on we now have the ability to check the density attributes within the protein uh specifically draw on pdb data to get those values and we can also visualize quirks for fun inside of finding atoms within the protein so if you've ever wanted to see what quarks might look like in Houdini this gives you a rough representation of them in the software uh we we also have two new amino acid hdas which allow you to visualize even more attributes of the amino acids and the proteins such as essential amino acids a non-essential amino acids any other particular data associated with them whether they're polar whether they're acidic things like that and then of course our aforementioned like backbone number than HCA update so this is a previous update from the previous 19 nodes in the toolkit uh which kind of only really allowed for basic modeling options and if you would like to see all the previous nodes in actin uh minus the ones they're just going to gloss over today I'd recommend visiting my YouTube page for the tutorials that I've created uh that will describe the specific attributes and characteristics of each individual node and also to our previous GridMarkets presentations where we kind of show them how to work how they work in an overall context uh these nodes also work extremely well with Houdini's box system and Karma rendering and they are fast and easy to load and only take a few seconds to generate a desired shape we will also be covering how to render these proteins and models today in Houdini and the overall new and improved Karma system in the software so let's get started and dive into Houdini so I do want to touch on before we touch on the file is that as soon as you download the toolkit there will be a few different things in this package one will be the various other hdas and one will count will be these three little folders one will have the instructions and toolkit information which has our credit of the hea information the instructional guide if you're more of a reader and then we also have some example data of proteins who touches with the software that we know what works so you can actually dive inside these folders and see all the pdb data there and if you go down here to demo files this is where all our demo files are so this is where you can actually open up a Houdini file and if you're not new to the toolkit you can just see an example of how they will work in the software so let's kind of get started this file that we're working in is that example build file that we just showed so if you were to open up this file let's touch on our older nodes so if we were let's say go to our space filling example you can just click on here and you can see that there's a space fill in diagram HDA already loaded up in the software and it's basically grabbing a pdb file which is this little protein Point Cloud so you can actually see the overall shape of the protein which is fantastic we're just transforming it to the zero zero zero World space so everything can be modeled in a more controlled area of the viewer so if we go and we add down this HD a state spelling diagram it will tell you how many you know Atomic counts are within that diagram there's 8 000 atoms in there and here's an example of some that you can actually see you can also if you wanted to control the size of different atoms within the structure if you wanted to make them bigger or smaller you can do that here depending on what type of width you want your atoms to have within the space filling diagram so this is one of our older nodes but you can also check out another older node which is called charge temperature animate example which is is this little node right here so what it does is it animates this protein by the temperature will the charge of factors and the temperature factors of the protein so we'll cover both once again we're using some cool protein information I'm gonna stop ghosting this so you can kind of see it's this big giant blob we can't really tell what's going on in this protein we're transforming it back to World space so we know that it's in the exact location where we want it to be modeled and we're going to drop down this really fun older node that we've built into this toolkit called Atomic property HD I always put this down so uh we can set up our base attributes across our atoms and if we go to our geometry spreadsheet we can see that it generates the electronegativity density other cool attributes inside the protein so if you wanted all your Atomic properties to be placed on your protein you can use this node and that's also going to generate our charge information so we can animate this we also have something in the toolkit called Atomic ionic properties which allows you to see the ionic energies inside the protein so that's pretty fun and if we go over to our charge animates we can now animate the whole protein by charge so if we play this back you can slowly see the protein move over time and that's based on the charge in the protein and this node does the exact same thing but it all it bases this on temperature Factor within the protein as well so you can slowly slowly see the protein move and you can see which areas have the higher temperature factors in the protein and which ones have the lower ones and if you wanted to dial this in and make it more accurate like you can do this on all of our nodes you can go over here turn off hide all attributes find the temperature factor and then find the range of the temperature Factor so we know this probably isn't correct uh visually so we need to change this to 0.81 and the lowest one would be three point five three and now we have it more accurate visualization of the temperature in our protein and where it's moving and things like that so that's pretty awesome and now now that you've seen kind of a rough overview of some basic notes and older nodes that we've done previous presentations on let's kind of break into the newer nodes that we've designed for this presentation so let's cover the Salt Ridge the salt bridge unfortunately uh we found a file path inconsistency here so I'm just going to fix that real fast the great part about Houdini is that you can just copy uh files that you have in other nodes and then bring them into other areas uh where you're trying to model something else and it should inherit that file path correctly so if we just wait for this to load we should see a protein there we go foreign so you can see I've brought in this protein I have something called my Atomic property stuff which is applying all my element information onto my protein and then we have something called our salt bridge HDA I'm just going to double check why this isn't working okay so you might have to lay down a new node if this if you ever run into this issue all you need to do is drop down another HDA plug it in and you should be fine there you go so what this does is it shows all the salt Bridges and the protein there's two ways to model salt bridges in Houdini and once charged by charge and one for one Stipe will die by dipole interaction and you can also visualize charges on this now the thing is is that you can also have various modeling options with this node so you can visualize the points and they're it's being attracted to you can also visualize the overall points and over here we'll just export any salt bridge bonds that are happening along with the models themselves so let me kind of set this up this note up so you can kind of see it in action let's increase the max distance if there's any well we can tell you tell for certain there's no salt bridges in this protein otherwise it probably would have found them but let's just double check and you can see that we're grouping the sole producer kind of controlled by the greatest and lowest charges and two groups of amino acids inside the protein and so I'm controlling which charges to isolate and see if there's a bond here on the uh HDA and there's one so we'll move on to the next node or we'll we'll come back to that later if we have time and test it with other proteins the next thing we can do is go on to amino acid types and so this is going to Showcase the other attributes of in of the amino acids inside our protein and you can already see it's working and it's creating a quite colorful model so we'll start at the very beginning here so our proteins adding our Atomic properties up and the cool thing about this Atomic property stop is that you can put the color on and that will tell you what type of transition metal or post-transition element it is things like that so onto our amino acid data Note if we over here we can visualize uh the unit die units of the amino acids so you can see the molecular weight and if we go to an amino acid groups we can also see uh which amino acids are basic acidic neutral nonpolar and unique within the protein so those will turn on different visualizers visualizers for you right here and if we go to weight and pH levels we can turn that on here and see the overall pH levels inside the protein which is fantastic and you might notice that some of these nodes have three different outputs so if we go over here this will output a model so if we're visualizing any colors such as the acidic proteins in here we can actually visualize them through our model modeling system now we can also go over here and we can visualize these bonds uh called chivalry Bond pronouncing that terribly but we can all ill create these little Loops in the protein to tell you which uh kind of atoms are not going are kind of will be located with those different attributes and if we plug this into the first input that will input all the points with the color information that you want also the other cool thing about this node is that each of these amino acid groups are also export with a group so if you want to isolate specifically acidic amino acids or basic amino acids later on post this node you can do that as well uh now moving on to amino acid types this is the ones a little bit different uh we're just going to make sure all these visualizers are turned off properly this one allows you to visualize sulfur atoms and this one also visualizes all the non-polar amino acids if they are any in the software and not software in the protein over here you can also once again view any positive or uncharged amino acids things like that or any amino acids with a negative charge so over here you can visualize any proteins that are associated with bodily functions in the human body so any a non-essential amino acids conditional amino acids or essential amino acids uh that are needed for bodily function so that's also something you can look into with these tools so let's move on to some other ones so let's talk about hydrophobic forces so one cool thing about protein modeling is that water is not really your friend but you need to know where water molecules exist in fat protein so once you've loaded up your protein into Houdini we can go over here to Atomic properties make sure those element attributes are placed down properly and you'll move on to our hydrophobic forces so it's already doing something and so we'll just turn off these visualizers and go one by one and explain them so if you turn on uh color water on this will tell you where the color uh not color uh water molecules are in the protein so you can see a bunch of points that have turned red and they're they're a little bit hard to see so I'm going to hit D in my viewport and kind of go over to geometry and turn on my point size so you can actually see the red dots more easily and also see where the water is in the structure so we'll turn that off and once again you can see any neutral polar ones and you can also see any hydrophobic acid molecules within the protein as well and once again neutral nonpolar ones so this really helps you figure out anything that water may or may not bond with in the protein and where those other amino acids might be located so once again this has many different outputs so over here I'm going to turn off my point size and turn that back down to normal I'm going to just keep on this visualizer for now so you can kind of see what's going on here so I'm going to turn all of these on there we go this is very very Christmas tree and basically I have this little out for lighting here because this is out putting all of my points in this PCA if I go over here this this output only outputs the water molecules in there this one only exports uh the hydrophobic acid this one only exports the neutral non-polar and this one exports the neutral polar so all of these exports or how our exports or outputs whatever you want to call them export different parts of the protein so the next thing we want to check on is our density Checker so our density Checker is really cool it's most mostly based around math it does all the math inside the protein so it takes a while to load up but allows you to see the overall Atomic density per amino acid within the structure and so you can see the most dense areas of the structure so I'm going to double check my Atomic density attributes by going to the spreadsheet and I'm going to Atomic density it's not hide all attributes and we'll look for it so we are looking for density and this one goes all the way to 4.8 or 2.8 and the lowest value is this so if you turn this on we can see that really the heaviest parts of the structure are those little red atoms right over there and most of the protein is located uh in the average kind of density range if you go over to the values here this will tell you the minimum maximum density within structure uh the sum Atomic density the average atomic density and the total density overall and a total atom count of the structure so it really does a lot of mathematical value calculations behind the scene and if you wanted to keep track of the protein Data Bank weight overall weight of the structure when you bring this data into Houdini you can just go to the protein Data Bank page find the structure weight and plug it into there so the calculations are a little bit more accurate later on it will also up this node will also apply this value onto your structure so if you're working with these points later on post this HCA and you need the structure weight in your calculations this is where you would add it into your structure so let's talk hydrogen bonds so hydrogen bonds are fun uh and I want the wanted this node to help visualize the hydrogen bond count of the protein uh dependent on the amino acid so if we isolate this amino acid and I'm isolating Serene we can kind of see if we go to visualization let me turn this off different aspects of this one amino acid so we can actually see the total hydrogen bond acceptor counts which will have to actually dial in over here if we go to apartment thing and this total each one on this amino acid has a value of four so it's going to remain yellow for now and we can also look at the overall hydrogen bond donor count of this particular amino acid and rotatable bond count of this amino acid as well so if you wanted to see the overall kind of bonds of the structure you would just turn off isolate amino acid and things like that so it's actually a very useful node for looking into hydrogen a little bit more in the structure now the next thing we're going to look at is our ionic bonding so we're going to look at ionic bonds within proteins so we're going to check this protein for ionic bonds to see if there is any there isn't that's okay but we'll just make sure we'll just look for them I'm actually just for fun I'm going to look for a different protein let's try this one transform it back to the origin it's a world space and there we go actually in this protein we do have an ionic bond so you can see how it's modeled these ionic bonds and then the protein by coloring each individual bond in a different color so it's looking to want to actually visualize the charge color so the blue would be the lowest charge and the orange in this case is the highest charge that this ionic bond is forming with so that's how you can possibly animate this now the other cool part about this note is that after you've you know animated your ionic bond before you do this you can also drop down a and you know animates if we can find it and we can actually add animation while we've modeled this Bond so if we wanted to show like how this could move well that bond is currently there and how it might change based on the animation we can do that right here as well so that's pretty cool and those are a few different nodes that we've kind of done in a Houdini I there's also a few other nodes that we've added into the toolkit where this is a post post processing node so if you wanted to apply any other rendering attributes onto your protein to make them less visible or give them Alpha channels or P scale or any kind of finishing attributes you can do that with this node so I'll leave that up to you if you want to even add extra colors onto the protein you can do that as well so if you crank the alpha up so one we can actually see the Browning noise color of the overall animation here as well so it gives you lots of different rendering options and we also have this cool little fun node called nanotube fun which allows you to build nanotubes it's mostly built off of a great tutorial from my friend Stuart but I had to put it into because he's done amazing work for the scientific Community when it comes to protein rendering so he's kind of responsible for this little tool but let's cover how you can possibly render proteins in Houdini so let's kind of go down here to the stage context this is where things can get a little bit crazy karma is currently in a testing stage so it's not fully Studio ready yet but it's certainly in a stage where you can start to use it locally and with your own personal computer at home it's also compatible with USD so if you like USD workflows USD is something that you can use with Karma so karma is a little bit different from rendering things in Houdini with Mantra you in order to render something with Karma you have to set up a whole new node tree that involves the geometry that you'd like to bring in right here the material library of the materials that you'd like to apply you have to attach your lights your camera and then set up a whole render system so you're building a whole node tree post uh building whatever objects you've just created so what we need to do if we're going to build something like this and in order to make sure this nothing bad happens I'm just going to slip Houdini into the manual so nothing happens when I skim through this Frame so the first thing in a Karma uh kind of system is that you've dropped on a soft crate are like using these because they allow me to just import whatever I'm modeling and also double check to see if it's you know able to render if there's anything I need to clean up or make any final changes too so I've used an object merge to merge in a protein example here and if I switch switch this over to auto update it's just importing the space filling diagram so now I'm going to jump back up again and I'm going to go to my material Library so materials in karma are a little bit different than mantra and they're they use something called m t i x standard surface and you have specular options transmission options subsurface options you have a wide variety of material options that you just can't get with Mantra so it's definitely worth exploring if you have a lot of time there's even options for thin film and also thin walled options if you want something to be super transparent if you need to like use the space filling diagram and then apply an alpha channel to it and make it look like jelly and then kind of have a render where you can see the atoms inside your space filling diagram you can definitely do it with these current settings that I have on my material now in order to translate uh transfer any colors from your geometry or any attributes from your geometry onto your Shader you have to use something called Mt LX geometry color which will bring in your color attributes and you do have to make sure that you're using color or float or color four depending on what type of attribute you are trying to transfer onto the base color so just be aware of that so now we'll go down to the dome light over here and this is where you can set up your lights so you can actually create lights you can initialize certain parameters you can color the lights deck of colors there's some really amazing options and you can also transform it into the light into 3D space like usual and then there's different other cover rendering options depending on what light you're creating for dome lights these are automatically turned off but if you're using a distance light or an area like it'll probably be on and you'll be able to use these Karma settings no camera wise the these cameras are the exact same that you would use in a regular Houdini object workflow same settings same view setting they just look a little bit different and down here this is kind of where the magic happens so karma is incredibly incredibly useful it renders things in real time which will cover very very briefly but very very soon in this presentation uh in these kind of Commerce render settings is where you turn on the resolution of your camera you'd reference the camera that you want to render out of your render settings which is this node you know choose where you want to Output the picture I wouldn't really change this directory by default Houdini creates a render folder for you whenever you go to render something and then names it the name of your file and also the name of your render node so if you remember to render rename this render protein it would render the image with render proteins so you can also choose your pixel sample image output options deep output if you need that for creating some really detailed protein renders there's also options for aovs as you can see here all that fun different stuff even at the SS options and lights and emission tons and tons of options there feel free to explore them on your own time we don't have a lot of time today to cover them all but now we can kind of showcase you right now uh the live app the live like real-time aspects of karma so I'm going to switch this to auto update and I'm going to make sure my materials are turned on my viewport and my lights are turned on in my viewport and I'm going to look through my camera so you can see this protein and I'm going to hit Karma and this is going to bring up the real-time render of Karma so as you can see my protein is rendering in the viewport real in real time and if I was to change my camera angle and rotate around this image it would also update the render to match the camera angle as well so currently you can see it's a little bit slow but that's mostly due to we're streaming and Karma is generally a lot faster when you have don't have any other applications open but it's a really fun and useful render tool for rendering transparent objects Karma has a really strong ability to render transparency anything that looks like gelatin pyro anything you can really imagine with volumes or transparency which is really fantastic there we go and as you can see when the first part of the render kicks in it will then start again at the center of your screen and slowly go in and again and again to kind of start rendering the finer details of the overall materials on your objects and things like that so I'm just going to turn off this render and you can do that by going to hitting GL and that will stop the render from happening so before anything goes terribly wrong I'm going to save and we're going to talk about how you can export this render into GridMarkets system so if we go over to Output here the first thing you'll want to do is drop down a USD render and you'll want to drop down the GridMarkets render submit note you want to attach your USD render into the top of the render submit node and also Define your lock path your render settings or camera you want to see through the output to where your image is going to go and all of these should be referencing this node here on your karma render site so all of these settings render out put and render output picture camera even a resolution should be referenced to your GridMarkets node and GridMarkets snow green markets needs your driver settings to be set to Husk in order to work and if we I'll go over here we also need to set difficult verbosity and that should work just fine and from here you can also choose to render your entire frame range or render a current frame and then the next thing you'll want to do is just double check your render submits I always like to make sure this project name is the same name as my example build or files so in this case my project name would be example build but if you're working in any other project with a different name put the project name in the project name area and then also list your artist's name as whatever your name is and then from here if you want to override any selected frame ranges you can do that right here as well I like to make sure if I have a specific frame range getting rendered over here I would like to copy parameter and paste relative references into here so this will always render the correct frame range that I'm working with and then the next thing to do is just hit submit render and that will submit it to the GridMarkets firm so you'll uh Houdini console will appear and it will tell it will say in this case if I'm able to connect invoice and that unless if you don't have Envoy open uh this will happen so what we'll need to do is Envoy startup GridMarkets Envoy that will load in the background and they'll load up any projects that have happened so I'll just log in and I'll look into my projects and now it should work and you can see the GridMarkets starts up and you hit save and continue and go and everything should work fine and usually if there's any other errors it will appear in this Houdini console and then this play in this case it says success the mission started and it will tell you where all the file transfers and that's pretty much it uh thank you for participating in this presentation today and I hope if you have any questions please ask them at the end and I hope you enjoyed it thanks so much Kate we now will have time for a q a and we're going to jump back over to Mark to run through the questions that have been coming in during the presentation we have a question let me read it to you so all right will the Houdini protein toolkit continue to be open source uh yeah it will be I think like one of the benefits of just having the signs toolkit is making it as open source as possible so people from the community who are using it can tell us like what is wrong and what needs to be fixed and what could be better so I would always like it to be available to the general public to test as well as on GridMarkets website so people can see how it can be used with like Cloud rendering and everything like that super okay another question how specialized is the toolkit for protein rendering I wanted to visual be able to visualize as much as possible with protein so it's very much in the like the very like animation light animation modeling stage and visualization stage where you can visualize parts of the protein and isolate them and say okay this is what this is what does what in the human body when it comes to like essential amino acids and things like that which might not be needed when it comes to protein folding or things like that to save different parts of the protein so it's generally kind of being made right now with the idea that any as any kind of kind of data scientists out there who likes to visualize things with proteins that you can use it and it will try and be adapted into your industry little bit more all right there's two more questions is there any are there any plans to make some custom materials or shelf tools for the toolkit all right uh so the next kind of stage I would like to do with this toolkit is to make sure if you're a beginner in like protein rendering or you want to get into the scientific field of visualization uh you can have a good starting point where if you want to start rendering things and you don't really know how or you're maybe an experience visualization artist who really wants to use udini who's never used udemy before I really want to work on creating presets for the tools so you can kind of bypass like you can still use all the available knowledge that you've curated for yourself all the in the past years but you can also use this toolkit and the presets to kind of jump hurdles over learning in the software so what shelf tools are in Houdini would be at the top of the screen which you kind of saw from my presentation there's a list of all these tools available tools in the software and in these tools you can basically click them and it will create an automatic setup for you and I would like to do that with the toolkit if possible uh so people don't waste time and meet their deadlines when it comes to visualizing something and material wise uh Karma materials are still in their infancy and there's still tons of things people don't know about Karma so I'm making presets for karma materials for kind of protein visualizations would be in a big interest for me because people can use Karma more for visualization okay and uh excuse me one more question it's a lot of interest Kate are there any plans to make protein modeling faster yes I'm trying to what I'm trying to do is optimize a tool is best I can and it's hard to do that when you're working with the data that you're bringing into Houdini the biggest problem with optimizing modeling in the software for Houdini is basically the size of your data set so I'll take the PVD information for example uh when you bring it into Houdini it's not one meter wide by one meter wide usually some like pro protein scales when you bring it into the software with the point Cloud can be over like 50 meters wide so you if you were to model something 50 meters wide uh with the tools and you had your own custom setting on there and you have let's say the voxels for for kind of a space filling diagram set up like 0.01 it would it'd be super high res of a model but it would take a lot of strain on your computer because of the size of data set so what I'm trying to do is kind of figure out a way uh when we bring information into Houdini because every single software has different units for scale and size to kind of create an HDA or a preset that takes the information coming in and rescales it to something that's a little bit more manageable because that's something I've kind of learned from the film industry they also have hdas and tools and workflows to do that and prevent issues like that from happening when they come into the software so that will probably be the next step that I'll be working on to better optimize like the models and things like that cool and one more question in the atomic properties node are the properties calculated on the flyby Houdini or are they taken from the pdb file so a little bit of both so when the information from pdb comes in it does have information for the atoms that are in the protein but it doesn't have any information associated with the atoms there's some but that's mostly in relation to the chains uh the amino acids things like that uh so what I've had to do is I've had to code all that information into effects and personally I want to go back later uh because there are Priceline data sets available of the periodic table that you can bring in and apply to things like this that probably would make the calculations a little bit faster uh but as of right now I've just found that Vex is the easier way because once you work with something like an external kind of file or external data set outside the software you have to make sure that people can always access it in the toolkit and make sure that the file directory is to go find that information are correct and sometimes that gets a little bit tricky so right now yes the calculations are all done all right Kate I think where this is the big finish I'm going to show our final slide so just a moment all right so Kate you mentioned that the protein visualization toolkit is on the GridMarkets website here it is here you can find the the actually you can find the prior version and the current version there and you can also find it from from Kate's website as well we have another webinar coming up with Kate so this is number four if you haven't seen the other two you can go to the GridMarkets website and look for webinars and you'll find all three now of the webinars that we've done with Kate and the fourth one is coming up on April 26th 9 A.M Pacific time go register now you can webinars hope to see you there and if you'd like to stay connected in the case of GridMarkets you can contact us using contact or visit our website and Kate's contacts are listed there as well and Kate uh that that URL is also where they can get the uh the protein toolkit from your site great super okay I think that's it thank you so much for joining everyone Kate it was awesome as usual looking forward to speaking to you again in April thank you have a good rest of your day everyone bye-bye.

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