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Kate Xagoraris



Time Feb 17, 2022 8:00 am. PST: Scientific Visualizations with VFX/science Artist Kate Xagorais

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. In this webinar, Kate will be showcasing how to visualize proteins associated diabetic functions in the human body. Watch this webinar to learn the techniques and technologies that Kate uses to create her compelling molecular visualizations.

Download the Houdini Protein Visualization Toolkit referenced in the webinar.

See HERE for our other upcoming webinars.  


Webinar Transcript . . .

Let's get started with today's webinar. I wanted to take this opportunity to welcome and thank you for joining us for our GridMarkets pharma webinars featuring powerful molecular simulations and screen tools. Today's webinar, “Scientific Visualization”, is the first of our two-part Scientific Visualization series. Over the next hour we're going to explore how visual effects artist Kate Xagoraris transforms molecular simulations 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 specifically this webinar will cover an introduction to Houdini an overview of how to export molecules into Houdini and a description of how to measure and model proteins with Houdini my name is Wendy Niemann and I'll be your moderator for our time together today we'll start out with a couple of brief presentations from Mark Ross with GridMarkets and Ben Hill with Oracle and then we'll hear from our feature presenter mark will discuss GridMarkets’ molecular simulations and screening service and Ben will cover the highly secure Oracle cloud which powers the GridMarkets service then we will 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 be sure to drop those 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 GridMarkets GridMarkets offers a secure molecular simulation and screening service which mark will describe in more detail thank you mark for joining us today thanks Wendy thanks everyone for joining today i'm going to give you a quick overview of GridMarkets and the service that we provide as Wendy indicated you can use GridMarkets to securely run simulation molecular simulations and screens at scale the solutions that we support are MOE Amber GROMACS Namd Quantumbio and Surflex. the advantages of the platform include the ability to accelerate your drug discovery process and how do we do that we give you the ability we give you the ability to select between one and hundreds of concurrently running machines and machines that are very powerful up to 96 threads per machine also you can leverage our unlimited MOE tokens if you're a low user and amber licenses without impacting your local license count so we use our own licenses and tokens not yours and you can run simulations in parallel as many as you want so this would helps to eliminate local machine lockup also the the other advantage of our service is it allows you to shed fixed costs you don't have to make investments in machines you know there's not expensive infrastructure and so and you only pay for the machine seconds that you consume the pricing is all inclusive so it's by the prices by the machine hour and there are no fixed or upfront fees and importantly the other advantage of the GridMarkets platform is that it allows you to focus on innovation not on infrastructure administration the setup is super easy it takes less than five minutes with three easy steps I'll show you what those are in a moment no special skills are required no training and you can submit from your simulation software meaning you don't have to learn anything new if you you can you can use the software you're already familiar with that is so let's see how it works how the setup works again it's three steps so the first step is to go to our website which is at the top there and you create your account after you create your account you download a tool called envoy which I'll explain what that does in a moment and you install that and you're done with the setup after you've installed envoy and now you're ready to submit so literally as I said a couple minutes to to get to this point now that you're set up you from within this example is showing MOE so this is a dialog box that appears within MOE when you're ready to submit a MOE submission and you fill out this dialog box with some basic things like your project name your submission name and so on and then as I mentioned you pick the number of machines that you want to choose for the submission in the red box there is a slider and you decide how many machines you want to use for this particular submission and after that you hit submit and that's it easy peasy when you do that envoy will then send your submission to one of two secure clouds either the Oracle cloud or the amazon cloud we're going to hear again from Ben today about the security of the Oracle cloud so the GridMarkets platform will route your your submission automatically for you you don't have to worry about the cloud connection we take care of all that for you after that happens we allocate the licenses in this case again the example is MOE so we're allocating excuse me the MOE tokens that you need to run at scale these tokens are not these are our tokens not your tokens so your local tokens remain available for you to use and you can scale up to as many tokens as you need at that moment then as your job is running real-time updates come down to envoy and they're displayed for you to to keep track of your job and here's what that looks like this is the screenshot of that so this is an envoy screenshot and it's showing in this case that you have two jobs running at the bottom there one is running and the other is waiting you can click on those jobs and find out the details of those jobs so if you want to find out what the status of the running job is you click on the running icon there and you see the logs in this case for MOE that's running at the time so you can go all the way down to those logs if you want when your job is finished the the results will be passed back to envoy and installed or deposited rather on the whatever local storage area you have designated and that's it that's the end of it so let's talk about what are some of the differences between this approach and the more traditional approaches of building a cluster or building something on top of an IaaS infrastructure as a service solution versus the GridMarkets option so firstly the setup as I mentioned the setup is in the GridMarkets's case is super easy takes three steps whereas the other two options are much more complicated to set up also the ability to scale your tokens or your licenses is very limited in the case of the local cluster or the iis option it's limited by how many tokens or clusters you have in our case we have access to unlimited numbers of tokens and licenses so there's no no limit there you can scale machines very easily with us you scale as needed and the local costs are obviously limited to by how many machines you have locally and what your quota is in the case of an IaaS solution the setup cost in the case of GridMarkets there is no setup cost it's free to get started your account to set up your account is free those steps that I mentioned to you and envoy those are all things you can do with with no financial risk we also give you I didn't mention some some a free trial as well so you can try it for free and and see how it goes so no financial commitment at all to get started whereas it's a pretty significant financial commitment for the local cluster and you know some commitment financial commitment to for the IaaS option same for maintenance the GridMarkets option there's nothing to maintain and therefore there's no cost to maintain it there's no no people required or special skills to maintain it it's very easy and the usage cost as I mentioned it's all inclusive it's on a per machine hour basis whereas the in the case of the local cluster it's predictable you have control over that but it's high and in the case of the infrastructure as a service solution typically they are unpredictable you get charges at the end of the month for data egress and data storage and so on which you can't predict in advance or at least are hard to predict in advance so the GridMarkets cost you can actually predict it up front you you know exactly what it's going to be whereas the others are much more difficult to to predict and lastly in the case of the return on investment so in the GridMarkets case you only pay for it as you use it therefore it has a very high ROI whereas in the other cases not so much so so if you're interested in more details this is our website if you want to send us a drop us a line for questions you can email us at awesome thank you so much mark our next presenter is Ben Hill. Ben is based in Seattle and is the global director for Oracle cloud infrastructure at Oracle with more than 15 years cloud architecture and product management experience Ben manages a global team of cloud architects responsible for supporting clients with all things cloud related Ben is going to briefly share with us the security Oracle brings to the table over to you Ben thank you so much Wendy so again my name is Ben Hill and i'm based in Seattle so I'll run through this really quickly and talk to you guys about how we approach security as it relates to our cloud infrastructure services so when Oracle went about launching our generation 2 cloud offering our approach to security was deliberate and direct we wanted to ensure that it was always on automated architected and architected in and best of all free so let's go through some of the high points on how we went about doing this first of all more security by default now what exactly does that mean well we design for isolation which means we've taken the hypervisor and put it on the network layer this approach separates customer traffic which provides better security and performance and as an added bonus it reduces the risk of hypervisor-based attacks also Oracle cloud infrastructure OCI has what's called separation of duties which means Oracle admins have no access to a customer's memory space and as it relates to your data and associated storage services we have full encryption at rest and in motion as well as integrated backups for business continuity and disaster recovery best practices now let's chat a little bit about our auto detection and remediation capabilities specifically Oracle cloudguard and OCI security zones Oracle cloudguard provides comprehensive end-to-end monitoring monitoring for your cloud environments by continuously collecting and analyzing service configurations audit logs and other information and reporting its findings as problems based on either out of the box security recipes or custom security recipes created by your admin and to complement Oracle cloudguard Oracle has OCI security excuse me OCI security zones which provides a secure enclave with customer tendencies for the most sensitive workloads where security is mandatory and always on this helps ensure compute networking storage and database resources comply with security principles such as always-on encryption no public access and automated backups and as I said before most security services are free like multi-factor authentication for user access OCI bulk which can be used to store passwords ssh keys and certificate and unlike our competitors OCI welcomes third party tools you can you can use to federate your identity and access management management policies with your organization's centralized identity identity providers as well as sim systems like splunk and logarithm all right that's all I have Wendy I will send it back over to you quick and fast awesome thank you so much Ben 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 VFX 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 scientific design in Houdini a Houdini user group for VFX artists 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 welcome Kate and over to you uh thank you so much sorry about that so today we're going to be covering about how you can visualize protein structures in Houdini and we'll be specifically kind of focusing and how you can visualize proteins associated with diabetic functions in the human body this topic is pretty close to home for me because I have a few researchers in my family who specialize in dietary needs associated with diabetes and pregnancy so they were like the first go-to people I went to when we were setting up this presentation as they had all these scientific resources for me to check out so today before we go into all the structures we'll be showcasing just a little run down on diabetes on how diabetes kind of controls your body and what it is so there's two different types of diabetes but firstly it's a condition where your body fails to produce insulin or your prob or your body can't properly use the insulin it creates so insulin cr controls the amount of sugar in your body so too much or too less sugar can cause deadly side effects so swollen feet loss of limbs heart failure etc your body uses sugar for energy however too much sugar can cause damaged organs as we've just talked about insulin is produced in the pancreas and people have damage to their pancreas regardless regardless of their weight can also develop diabetes so the two different types of diabetes are type 1 which is specified as an immune to its disease and people with type 1 are not able to produce their own insulin and they are completely dependent on insulin injections they can also produce glucose however their cells can absorb glucose as they are a hybrid extremely high risk of high blood sugars type 2 diabetes is also caused by many different things in this case the body can still produce insulin however the cells cannot absorb it and people who develop type 2 usually have a family member with diabetes or are they are overweight or they are over the age of ten so there's two main different types and diabetes is such a global issue and so many people have it nowadays I thought it would be worth the cover what it kind of looks like at a molecular level so one of little protein I kind of wanted to highlight about diabetes is albumin which is a very key protein in the structure when you study diabetes it's a protein made by your liver it helps you keep fluid and other elements in your bloodstream so they don't leak into your surrounding tissues doctors usually measure the amount of this protein in your blood to detect problems with your liver and kidneys the protein will be breaking down today's associated kidney function but more on that later in high rest diabetic patients liver and kidney problems are very common place because often diabetic patients are peeing out blood sugar or sugar through the urine if they have too much sugar in their body or kidneys are really good fine just say okay is your diabetes under control or is it not so albumin also carries hormones enzymes and medicine throughout your bloodstream so if you have a low album level this can result in a lack of nutrients entering your body and your overall body mechanics shutting down there are different types of albumin and your blood and this includes blooming human serum albumin or shsa bovine serum albumin bsa which of the last of course is seen in bovines and extracted from cows this protein is also considered a globular protein and is water soluble and it has several keylesses that make it very rigid so we are going to be talking about pvd a lot today so the PDB is the protein databank and they can use a lot of open source molding mole data so we're gonna be talking about that each protein structure and that's stored in this databases has a unique id number and this helps track it each protein protein and pbd also has a 3d representation and lists their other molecules that are contained with the structure it does more than that there's also very helpful visuals on this site so I know if there's any scientists in this call they're probably very familiar with this site but just for the viewers who have never seen it before it's probably one of the best open source data things on the planet so today we are using a software called Houdini to showcase these proteins Houdini is a pretty graphic package that was originally developed and designed for visual effects and animation in the film industry it was first designed to be as procedural as possible and that's at Houdini’s core currently it's now used in VFX motion graphics virtual reality film and tv on top of that it's also used by corporations such as nasa for astrophysical visualization medical rendering and much more there are many perks to the software which is why it's so flexible and so enjoyable it processes a lot of data data faster than other 3d graphics packages such as maya so it's really a go-to place for entering accurate data in right now Houdini is extremely durable and a durable software it has fast and easy replication of objects fast simulation time python inputs and its own internal coding language to name a few there's one numerous academy awards for its development in visualization technology and also has a founding background in science one of the owners one of the first founders of Houdini and creators of benini he originally helped design simulations with Canadarm which still is used on the iss for this day the very day so it has such a background in science from its own creators and what they were developing in the 80s before they even created unity or prisons as it used to be called so there's a lot of thought that's gone into the software to make it what it is today one of the best parts of eugenie is this ability to combine modeling effects lighting and rendering workflows together so if you build something on the software you already have the built-in pipelines output everything you've created like creating and saving your effects you can also be working on light rigs correcting mistakes and previewing renders all at the same time you can one of the best ways of pd that we're going to kind of showcase today is that well something is thinking in the background you can also be doing a bazillion other things so you also have real-time feedback of what's happening in your viewport there's so many different functionalities of the software it's kind of hard to explain all in one lecture but we're going to try Houdini also has an awesome python interface but you can import your own apis and other tool sets with use so if you're a very python oriented person this is also a software for you because there's python shells there's python wrangles there's python nodes there's tons of different ways to make sure your code gets implemented successfully when it comes to visualizing scientific data Houdini is great for importing point cloud information and processing attributes it works with a range of volumes in vbd formats and it has several different nodes that can help you isolate values attributes and groups these processes are fantastic for keeping your theme clear of information that is cluttering uh one of my favorite parts of Houdini is the ability to input waves animation and point information and velocity fields which you guys could guess you could say is a lot of different elements but let's kind of start with waves and animations first one of the internal functions of Houdini is a system called chop chox is a channel off called or more also are kind of also called channel operators and these allow you to add wave functions into your animations for faster and easy procedural movements they also allow you to build an input wave system for musical instruments sounds and wave patterns with smaller objects such as atoms there's a few examples of the heating community creating tool sets and accurate examples using chops such as quantum material electron waves within the software so when chops is really useful because not only can you import waves wave functions into the software that allows for that ability but you can also kind of animate something in the software and export it as a wave function through chops so there's other tool sets particularly the Houdini musical tool set that allows you to actually animate let's say a bouncing ball in the software and then output that is a musical sound through Houdini which is a mind blowing the interface applications of Houdini also allow for quick and easy changes in case you need to add your own attributes sliders drop down menus and toggles combining this with its animation editor it also allows you to promote different levels of parameters and view animations at the same time bringing in point information to dimi is incredibly simple Houdini expects a different range of formats as we've talked about and its geometry spreadsheet allows as like for a quick and easy solution for viewing strings primitives and point in additional attributes so one cool thing about Houdini is that when you view any attributes on any object it separates them all based on the information associated with which we'll kind of get into today uh when you play back the timeline of Houdini you can also watch how the attributes on every single vertex point in primitive and polygon change over time it's in real time as well so let's say if you need to work on velocities or pretty much anything that involves motion the lenovo allows for quick and easy setups of velocity fields and internal volumes in its internal volume system and it also allows you to infect points of these fields or even fluids kudemia is not only only allows you to create physical accurate simulations but it also allows you to quickly replicate anything you create as well so one downside to using pvd data or mold data in Houdini once you enter it is that you won't be able to measure distances of bond angles unless you create a custom-made system which we're going to try and showcase today which but you can use stops and VEX nodes to achieve this most scientific visualization packages have specific tools for this but Houdini is special where it just allows you to customize and create your own tools based on what you are trying to achieve so you can also use Houdini to create custom renders and cinematics which is very easy to do Houdini also allows for you to simulate structures as well but once again you have to make custom-made systems to allow for accurate atomic movements and again you can do this through VEX or vos today we'll be covering the boss method Houdini is great at displaying wireframe and space filling diagrams of structures as well a great resource to kind of work in tandem with dvd and Houdini is protopedia they give detailed breakdowns of human protein structures and 3d examples of them as well but before we kind of demonstrate how to use this database and also all the data inside of me I also want to give out some shout outs to the Houdini community of people who are already headed down this road of visualizing protein information inside the software the first show kind of goes to the wonderful team at pentagoma and Entagma is run by two wonderful artists named manuel and morse and their site is probably one of the best Houdini run sites in the world and it's great it's a great it's a great starting place if you never worked with the software before and they also have wonderful segments for visualizing the chronobytes spike protein with dr jerome claus and they also have a great podcast on how to translate scientific documents in this release space so I highly recommend stopping by them if you're new to Houdini and you want to achieve what we're going to try and do today inside the software the next shout out kind of goes to another artist named Stewart Jansen he runs a channel called making bio cinematics he has a great youtube channel where he walks you through creating acne filaments and Houdini as well as other nano structures both of these places are great stewart also has a website which you can also check out which is linked to his youtube channel now let's kind of jump into the Houdini visualization breakdown so before we jump into the software we should cover the basics of the attribution groups you're going to see while we begin this demonstration we when you import your data into Houdini and jump into the Houdini spreadsheet you'll notice that there are tons of attributes that come in with the point cloud the first you might notice is the chain id element's name resume and res sequence and serial number the chain id will show you the main chains of the structure this can be a b or c or even b depending on the structure when visualized these protein chains will make up the majority of the system as like long winding lines the element attribute will also show up with different letters underneath it these letters represent the different elements inside the system so depending on the structure you might see the letters c o and n or more c stands for carbon o for oxygen and for nitrogen next up is the name attributes name corresponds with the element attributes so depending on the structure you might see others such as a n o c a and c or more underneath it sorry or even more complicated letters such as cg2 and cg1 usually nco correspond with the element name but the others will give you more individual information on the carbon variance cg1 for example is a carbon element but that's also containing its position information so after that is resname underneath this attribute we'll find a list of hyphenated letters for example g y l or g u l hu or even hoh from or more these represent the chemical compounds of the molecule and also the amino acids some of these represent sugar or glucose or other components so please refer to PDB or your other periodic table of elements when you are at this stage of visualizing your structure please selectively delete these chemicals if you want to still isolate different areas of the structure which we'll also cover today red sex sequence also corresponds with the red name however it displays the sequence number corresponding with each chemical compound this shows where it is in the structure serial also shows the total count of all points within the structure and depending on how you would like to animate your structure you can also take a look at the temperature factor attributes this will show you how solid each element is and how it behaves under certain conditions or values isolating data in Houdini is fairly simple it only requires you to create two lines of x to isolate any attribute or groups within the structure and in the demo today I'll be going over today we'll be talking about the issues HDAs we've developed and the code inside of them so we're going to be cracking them open as well as showing their top level structure these hd's are exportable and we'll kind of talk about where you can find them after the presentation so in this demonstration we'll both be covering how you can create a custom measurement tool within the software to measure the distance between each molecule as well as kind of give them a number so you can count how many amino acids are in a particular chain measuring where these molecules are is important as it's easier to understand how they interact with certain parts of the structure and this tool will also showcase how easy it is to isolate areas of the protein with little to no coating we'll also kind of cover how different parts of the structure and groups and attributes that are carried on the point clouds and where you can find them and how they kind of relate to pvd you can also group atoms by change they are associated with within the protein and we'll be severing these more when we create space filling diagrams and ribbon diagrams within the software one really cool thing about Houdini is it has these open source tools that come with it called side effects labs side effects labs contain some of the most advanced modeling tools currently with the software to make your workflows faster as well as containing tools that can bring information from other software and for texturing of effects purposes these tools are great for diagnosing bad mesh interactions or intersecting geometry as well as measuring the distances between points and 3d space currently a lot of the lab tools work with mocap (motion capture) information and open source world building sites like open streets maps however I also find these tools are also pretty great with pretty much any modeling or animation you might need to do in the software if they even if they don't relate to open source maps or even mocap so just a little refresher before we actually show our final file for the people kind of new to protein visualization there's three different ways you can visualize a protein these are space filling diagrams backbone or ribbon diagrams or wireframes wireframe should these diagrams show showcase each covalent bond between atoms space filling diagrams these are diagrams that showcase each atom as a sphere and backbone are ribbon diagrams these are diagrams that show protein chain holes so backbone diagrams just show a tube connecting each chain with ribbons the chains are showcased as helices these different diagrams are also used for different things so wireframe is great if you'd like to look at the small details of a protein structure space filling is great for seeing how proteins interact with each other as well as viewing the overall shape and structure of the protein scientists often like to view these diagrams because they are the most useful for showing how much space has been doing in between atoms as well as parts that might connect with other proteins so backbone and ribbon are also great for visualizing protein folding protein folding is a process that makes the protein active in its current environment so coloring your structure is also very important you want people to understand and distinguish each individual structure differently so you don't want a black and white photograph like this usually structures are colored from blue to red to show the beginning and ends of the change and it's also advised that color every different protein differently to reduce confusion between atoms is also a great way to it's also the best way to showcase the bonds between atoms and you can color different atoms differently based on their elemental composition so in today's presentation we will also kind of go over the simple color techniques you can use in Houdini and how to create your own custom colors for every individual structure of the scene Houdini is very flexible it allows for to blend you allowed to blend color attributes with different groups or attributes so if you wanted to build a shape filling diagram of a protein and highlight the hydrogen atoms for example you could absolutely do so so let's kind of dive into Houdini now it's time for the actual kind of demonstration of the protein we are covering today so we're getting ahead of ourselves here let's first look at dvd so this is the structure we're kind of looking at today it's code under pvd is for nes and it's an x-ray structure of human aquaporin it's on considered a member pro membrane protein and you can see like the four individual chains in this photograph here pvd is great because you can also get additional data for the atomic count of the structure as well one of the things that i'm going to continue to develop with this tool set is that as soon as you bring in this information in big uni you can also achieve an accurate atomical count as soon as the structure is inside of it as well as other residue counts and things like that or any additional information you might need to visualize the structure based on the other things we are going to cover today if you would like to download your individual mold data from huge from pvd and bring it into Houdini you can go to download files and click on the pvd format that is probably the best format to use when you're bringing in information in this bikini because it has all the information that you will need so let's dive into our files so we kind of have a lot going on here we have some space filling diagrams that are on we have some ribbon diagrams and we also have some interesting little atomical things going on over here so as you can see I've kind of separated everything individually and I can turn off different elements of the structure based on certain nodes so that's something that's really great about Houdini is that you can promote different aspects whatever structure you model to the surface so each individual one can have its own individual mode and you can just break it down like that so let's start with space filling diagrams and our space filling diagram HDA that we've kind of developed for the software so i'm going to be taking a look at our space philly d section of the structure on this side but let's jump up to the surface here where we kind of brought in our information so after downloading your files from dvd or bringing in your mobile data it's going to appear as a point cloud in the software and the point cloud here it looks very boring but there's a lot going on if we go over to our geometry spreadsheet which you can usually find at the upper kind of center area of your screen if we click on that we can kind of see everything we just talked about where we've got our chain id our element our name our occupancy our resonate and our red sequence as well as our serial numbers and our temperature factors over here play in the back nothing's happening because there's no animation on this model but we do have all the necessary data that we need to model this so the first thing you'll want to do when you bring in your information is kind of transform it to the center of the world so I have it transformed it down here so what I've done is I've taken a transform node and I've gone move centROId origin and that will automatically place it at the center of my world view and then I've kind of rotated the structure in a position that I've liked and that's what you kind of would do to get it kind of set up in the software so over here I have two different nodes that are going on and the first one is called remove sugars so I don't really need any sugars today in the structure so anything that has that that's under res name in our geometry spreadsheet if it contains this name or this string will be removed from the structure and then I've for my next kind of node is this is where it gets kind of fun where i'm started to isolate the different chain ids so every single chain if we go over to our geometry spreadsheet we can probably find it here you'll see a's b's and if you scroll down we got c and we also have g so we are just telling Houdini hey based on these strings so on the chain id call this b-a-d like that then I've kind of added a little null and those are really useful in Houdini they literally stand for nothing and they allow you just to put them down as placeholders or even if you wanted to store values inside of them you can absolutely do so like that so if you wanted to use them as controllers for HDAs you can also turn them into those so down here we have a few things going on we have these blast nodes for about every single node that is being exported down below and what these last nodes are doing is basically we're telling it hey find chain d and then delete it from the structure and isolate it for us so only chain b will be fed in these two HDAs and over here we only chain seawell a and b so all of them are being broken off and separated individually for our space filling diagram down here we have our space filling HDA so what the space filling hd is designed to do is give you maximum flexibility when you are modeling these structures it also allows you for different animation actions and also visualizing different elements on the structure so let's covering them let's cover the modeling tab first the modeling tab works with something called voxels so basically if we were to dive inside here we'd kind of notice straight away that we have something called vba from particles which basically what this node does it takes down any points that are coming in and converts them to a vdb or a volume based on what you'd like and then we've kind of converted them back to polygons so what what this fossil 5 does is basically controls the resolution so the higher the resolution the less detail the lower the resolution the more detail and that's really up to your own personal preference the point radius scale really comes down to basically controlling the shape of your space filling diagram so if you wanted less to control the spacing between each structure more individually you can do that with this tab the minimum radius and voxels it corresponds to the radius scale so this always kind of has to be smaller than your radius scale for it to work it's an internal thing in giving me that allows better control of your PDB so it kind of always has to be promoted to the surface this little color tab down here allows for customized colors of your space filling diagram so we'll just turn that back to what's its original color over here on the element visualizer we go element on we can kind of see it be different atoms or kind of atoms or different elements that we can visualize on the structure so if you wanted to visualize the nitrogen atoms we can do that here with oxygen and carbon we can also visualize the elements position as well so if you wanted to say okay let's look at cd1 we can find those on the diagram as well so there's different customizations of what you can visualize on the space filling diagram but it's really up to you for the animation we have two toggles for the animation on and off so by turning this to one that will start to animate the model and turning it off we'll keep it static right now animation wise this is kind of still in development we're gonna i'm working on a kind of point two of this tool set so you can import more accurate animation that based on the temperature factor of these models but right now we're kind of working with a noise interface so you can add your values into the offset panel here for whichever value you choose through your temperature factor and you can animate it by the frame range which is dollar f so by playing the amplitude you can also control that the breast mist and the turbulence so that's kind of the most that's how our kind of space filling diagram works it takes in the atoms associated with this chain animates it and allows you to customize the color and modeling and visualization of the different atoms within it so jumping back on to our surface level we're going to take a look at our ribbon diagram so the ribbon diagram HDA is really fun it has two different forms one is animated and one is illustration mode so illustration mode will allow for your to form your helixes but they'll be static and you might already notice something special about them there's different areas on these tubes that are highlighted and we're going to talk about that in a second but basically that allows you to find where each kind of amino acid is located on the ribbon or the chain so that's where they would be located so if we turn this to animated mode which are also isolated to the top level here we turn these on we should see something interesting and start to happen um you can see the structure kind of slowly moving over time and also animated like that so let's break down our ribbon diagram HDA so diving back into here you can see it's right beside our space building diagram so it is a reliance on our chain information that we bring into it let's start with the illustration most that will be probably the easiest to explain so taking a look at the structure over here we can go to our HDA scroll to the surface and there are three different toggles one is for the chain elements one is for the amino acid and one is for the illustration animation portion of it so let's start with the different channel elements over here there's three different toggles so these three different toggles allow you to pick the different elements that you want to form your chain with in this case we're using we've got these toggle options of nitrogen oxygen carbon and other carbon based elements and we can choose them from here going to amino acids what this allows you to do is visualize a different amino acids on the structure so if you wanted to go here you can see that things are located here and by swapping out this toggle you can find any of them located on them on the structure you can also turn them different colors so based on which protein you like if you want to keep them separated you can do that as well and depending on if this is an illustration or animated mode we're working with the illustrated mode right here so we keep illustration on but if we were at animated mode we'd keep animation on and you won't see if the animation color animated color appear on this particular null because the animation comes at the second input of the HDA so moving over to our animated slide we'll let it shoot anything itself out we can see that our amino acid toggle is on so we can turn that on and off and we can go over to our illustration animation here and we can play with basically the wire radius the wider radius of both the illustration and the animation we can also give them different colors depending on what you want for us maximum flexibility and if you want one of these lines to be thicker kadini will just kind of think itself out and make them bigger upon requests so there's kind of a real time feedback like that and then here is where you once again you put in your animated values if you wanted it to move and if you want to add noise in like a bass noise into the ribbon model you can do that with this kind of toggle right here sometimes pudding is special and doesn't want to respond when you play play it back in real time so there's a handy dandy reset toggle right here which will reset the simulation that's inside of this HDA so that's very useful if we kind of dive inside it there's a lot going on up here you can see that we have kind of a base rainbow that is figuring out the kind of strings of our name chain and also it's inputting these groups based on the name that we can control and then it's also kind of searching for the backbone of the lines that we can use which in this case is looking for those three individual proteins I mean a protein element sorry my mistake there over here we have kind of two inputs that are happening the first input is the kind of wire frame or illustration top toggle of the ribbon so this is the very static one with no animation at all and the second output down here is where the actual simulation happens and it's using something called vellum inside of Houdini vellum is very good at handling dividers or hairs or lines in structures such as these without massive collision mistakes so it's great for keeping something looking kind of organic in movement when it's being represented in a wire mode or a wire shape so it kind of just takes this line simulates it a bit and then down here is where the polygons or kind of structure is finalized and the colors are added jumping up to our surface we're going to be covering our amino acids and how those are modeled so if we turn them on all so turn on all of them you can see that there's a lot of them straight off the bat but Houdini loads them up back fairly quickly so they're all colored very differently and that's okay I don't have them on all of them on all the time when i'm visually visualizing a structure because there's just so many of them so for sammy sake and also for less confusion i'm going to turn off the majority of them while we're hunting around in the software so going over here to a little node where I've labeled data setup and diving inside this is pretty much all you need with to set up all these different molecules and it's just one HDA that we've kind of refined and also set up so you can visualize different parts of the amino acids so once again we're bringing in our kind of handy-dandy point cloud or mole data and we are transforming it to the center of the world making sure it's in the same position as a ribbon diagram space filling diagram because you don't want to in very different places and rotating it correctly and then we have we've placed put down moles to make sure the different streams of information are collected collected and exported successfully and for just for fun we're going to take a look at sur which is I believe serene the serene molecule so i'm going to change my viewport setting so you can see this better so i'm going to switch it from light to dark that's another great part about Houdini is that it's optimized for you as the artist so depending on which settings you want there's light dark gray and different background talks toggles and you have texture filtering options zoom or you can even apply environment maps in the background so it's great but heading back talking about about our HDAs again these hds are very simple if you dive inside there's about two different subnets the first subnet is actually just separating the molecules and finding the group to isolate so if we turn on our point visualizer it's isolating these random not random groups but these molecule groups across the structure based on this single wrangle which is isolating the res name and then it's taking this group over here and it's grabbing all the information from this toggle to find the serene molecule and then we kind of have a partition here just in case and then over here in this sub network we have a bunch of different things that are happening we have two different outputs this output kind of is focused on creating the connections between the and this connection over here is designed to isolate the atoms themselves so you can have better color control over them as well so jumping over to our surface level of our HDA we have three different toggling menus we have a molecule modeling connections and an element visualizer and this molecule modeling area allows for you to toggle animation on and we have our animation settings so in the offset area is where you enter your animated chosen animated values that you want these molecules to move by you can add turbulence you want amplitude roughness etc you can play with the voxel size again or the point radius scale of your atoms so if you wanted them bigger than their connections you can do that too back to normal and we can also color them different colors as well so this color is actually linked to our connections color over here but you can also delete this channel by deleting the channels between the colors and also coloring them differently so you can have different options when it comes to you know if you want to visualize where the atoms are on a connection you can do that as well so we're gonna just fix that here so over here we is where we would form our connections between our atoms sorry i'm just gonna take a good wire and you can see here there is a search radius of points and the max search point radius that you can play with over here basically what these two toggles kind of do the max the search points looks for the amount of points in the area and the search radius points creates the connection so if we were to lower this value our connections disappear and then the higher the values the more connections appear between the points so this is at your own discretion of how you would like to form these connections over here on our element visualizer we can once again visualize our element an element position so if we toggle these on we're not going to see the color because it's red so if we turn this to blue we can take a look at our carbon atoms oxygen atoms and our nitrogen atoms like that so it's really up to you and what you want to visualize and once again these puzzles also work for element position so we'll turn these blue and there they are so it's really customizable on what you would like to visualize and what different parts of the structure you would like to visualize as well so jumping out of this we're going to jump back to our kind of molecules or our amino acids and one big part of trying to visualize structures like these is talking about like how big the structure is and distance between amino acids and how they might connect or overlap with each other or how close they are to each other so we've also kind of developed this measurement tool that will actually allow you to count the amount of the do a proper count of all the amino acids that you'd like to visualize as well as the measurement tool to see the difference the distances between them this tool is currently working with these two amino acids right here val and trp and if we dive inside the tool can also work with only one acid we're working on a toggle where you don't have to use both you don't have to use words both acids at the same time but you can also play with just one and do an accurate count of how many there are in the structure so i'm just going to turn off these numbers so it looks like less cluttered for now and i'm also going to turn on show all objects so you can kind of see what's going on in the viewport here so this measurement tool actually measures the distance between this kind of molecule up here and this blue one down here Houdini measures things automatically in meters because it's canadian software but you can customize your measure measurements of distance within the software itself in the software settings which I believe are in your file or edit tab so just keep that in mind when you bring things into the structure they might look a little bigger on or smaller depending on its original size so through for this tool we have three different toggles we have distance acid one and massive two let's start with distance so distance tab is where you control your line and font color of your measurement tool so there isn't much to change here other than the line radius if you want to make that thicker thinner you can also play with the font size as well in the font color and the line size and the line color so going over to acid one what you can do here is there's a toggle where you can say numbers on and numbers on will basically give assign a number to every single molecule within the structure based on how many they are and then based on where your tool is and is pointing to it will also color the selective number it is involving in the distance calculation so in this case we've kind of told it to visualize the number two because that's the index number index it's grabbing for the tool if you want to change which kind of molecule you are measuring in the software if you were to change this to five the tool should update and find molecules five also will jump from two to five and now five will be highlighted and the distance will also be updated as well you can also play with the font size of the numbers and the kind of thickness of them as well if you wanted to render them um an index is also where you would isolate numbers that you'd like the next thing is an amino acid too so i'm going to turn off these numbers right here go over to amino acid 2 and turn this on and you can basically find out which ones it is highlighting so we have things going on here where we have it's isolating kind of molecule five over here and it's giving every single kind of molecule a different number as well and down here is where you can color things differently so the chosen number if you wanted to make that red instead of yellow you can do that for better visualization purposes and once again you can play with the thickness and font size it's really up to you with how you'd like to customize this tool hopefully in the future we're also going to be adding another function to this tool where you can not only just measure one particular amino acid or molecule but you can also measure ribbon structures themselves there will be a little toggle on our ribbon tool where you can measure just different select parts the structures based on other ones so that's kind of the hds we've developed and what is kind of in progress right now which is really great and kind of jumping back into our presentation i'm going to stop share and re-share my screen that was awesome Kate oh yeah we got more we gotta talk about our ideas now I think we're gonna we might have to pick that up in in the next episode because we've just run out of time we're at the top of the hour okay once you give a quick overview of this and tease them with what's going to come in the next in the second version of this webinar and then we'll wrap up from there okay okay sure so basically we've been developing these HDAs so you can find these HDAs that we've kind of gone over today and talked about on the GridMarkets website as well as my own site all of these ats work in combination with each other's and all of them are really particular and most of them work well with most proteins on PDB especially ones that are associated with human functions i'm working on something else with pvd-related data because I noticed that there's some proteins related to marine structures on the sites so i'm developing machines associated with those as well but basically we have four of them available the wireframe HDA the base filling HDA which the wireframe is for visualizing your molecules space filling the overall structure the molecule measure HDA so any one to two finish and model molecule groups to work and the ribbon diagram HDA which allows you to form those big keylesses so all of those are available in open source and ready for download the HDA package also comes with an example file so if you're not sure how to use them you can open up the example file and see how everything is set up within the file to get them to work and the package also comes with pre-downloaded data so you can have some example molecules to model as well and that's pretty much it I'll hand it back over to mark thank you so much Kate that was an amazing presentation and a beautiful presentation as we are running short on time today we'd like to encourage anyone who has any questions to please send your questions to us via email at we look forward to seeing you in may for the second of our scientific visualization series webinars where Kate will pick up for where she left off today watch our website link for exact date and time details and in regards to that do you have a simulations visualization challenge Kate GridMarkets and Houdini can help solve if so drop us a line again at that email and we'll visualize it for you during our next webinar in may also be sure to save your seat for our march 15 webinar featuring new chem sciences and their presentation molecular modeling in the cloud a turnkey solution for scalable sims registration can be found on the upcoming webinars page of our good markets pharma website again thank you very much for joining us today we look forward to seeing you in march and may for our next GridMarkets pharma webinars.

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