 Good morning everybody and welcome to the BioXL webinar series. Today's speaker is Miwosz Pichor from the Institute for Research in Biomedicine in Barcelona. Milosz, we speak about molecular movies made easy with mollywood. Now, let me tell you something of the today presenter. Milosz is a Marikori postdoc in Barcelona and Splisity is working in a molecular modeling and bioinformatic group of Prof. Modesto Orozco in Barcelona, the Institute for Research in Biomedicine. He got his PhD in Ganche University of Technology where he worked on interaction between turmeric DNA and proteins, but also he was using free energy calculation machine and classical quantum mechanics and classical models together. So, when he was involved in so many projects, he got interested in visualization. In particular, he noticed that all the articles were at very bad representation on the molecules and the molecular structure and one can understand a lot by visualizing better a molecule. So, he decided to put a lot of effort also in developing and improve visualization tools. But in the meantime, he's also went on with his own research that is on DNA damage, epigenetic, and also on the development of tools for improved classical force. And now I will give the world and the presentation to Miwosz. Okay. Thank you Alessandra for this beautiful introduction and thank you to the Biaxel people for letting me give this webinar today. Okay, so this was a side project and it remains a side project that started growing and growing kind of out of control that in the end what we hope to achieve with this project is to help the community with something we've been struggling with for a while now which is making of molecular movies. So, to give you a bit of a background, what really happened actually almost exactly two years ago, it was November 2018 and I remember I came to Barcelona for the first time coming from Poland. Quite wasn't a surprise by how nice the weather was right there. And I gave a talk about what I was doing during my PhD. And after the talk I was approached by Adam, who by the way, recently gave a great Biaxel webinar on the building blocks. And Adam asked me what tools I used to make the movies for the presentation and talking for a while we agreed that everyone is just writing their scripts from scratch. There's actually very few common tools that we can use. Most of them are just Python TCL libraries that are bundled with the visualization codes like VMD or PyMol. And so you can either do very simple things or very complex things. And if you know some blender and blender Python interfaces augmented by no VMD exports and so on, you can do really amazing things that you could see in the movies like molecular life of the cell, something like that. But then if you want to do something that is right in between, so it has a bit of complexity, it has some labels, it has some nice graphs, then you either have to spend a week developing your own tools or there's just no other way to do that. So when I was working on wrapping up my thesis then in March, you know, when you're wrapping up your thesis there's nothing better than starting a new site project. So I started playing around with the scripts I had at the time, trying to put them together, trying to make something as original as possible out of them. And we tried, so I was working also with Adam asking him about all sorts of input about how we should proceed, what features should we have, how we should develop these things. And we agree that we should have simple syntax that is separate from any programming language. We should have a lot of documentation which we now have as we show you. And we're trying to follow two guiding principles, so first make it plug and play so that if you want to start using that you just download it, you install it and it's set up in five minutes max. And on the other hand you want to follow the famous guideline of making easy things easy and complex things doable. So if you want just to have your simplest movie that's literally showing short animation that should be doable in five minutes, or maybe two minutes. On the other hand, if you have a plenary talk at the conference and you want to have a two minutes movie that has a very intricate plot and some extra panels and lots of things in that. You can also do that if you put enough effort. So that's an idea of what are who our target users are we're trying to target people at all levels of expertise in the computational field so whether you're an undergraduate student, or whether you're a postdoc or a professor, you should be able to to benefit from the tool. It should mostly should suit all your purposes, maybe if you're trying to do some super cool feature video for for nature maybe then you should go to something like then there's something level higher but I would say for all the vanilla applications, our tool will will be sufficient. And then our goal here, our broader goal was to, you know, make movies, more like figures in the sense that when I make a publication I usually make six to 10 figures, and just maybe one or two movies. And the idea would be maybe to balance those things out I don't know what other people think about it but I would love to, instead of seeing like an arm is deep lot. I would love to see a movie where the arm is deep plot is shown alongside with the molecule that's actually moving. That's the simplest example possible that we should also try to push on the journals you know to recognize movies as an acceptable way of disseminating science. And obviously you want to have movies for all your YouTube channels, vlogs and things like that for for all sorts of popular science goals. So how do we do that the idea was to make movie design fun, as opposed to make them make it tedious because normally you would spend I would say 20% of the time designing the movie so deciding what should go into the movie what you want to show and so on. And maybe 80% of the time in actually trying to implement all those technical aspects, putting things together, writing loops, smoothing things and so on. So we wanted to invert this proportion so that you can spend maybe 80% of the time designing the movie thinking of what should go in there and making it more fun to watch and for fun to design. And then the 20% or maybe even 10% of the time, you can spend just running the actual script, or dealing with the technical things. So we tried to keep the structure of the tool as flexible as possible you know to let you experiment let you be creative with all the options that you can think of. So if you have an image in your mind, so you want to convey this exact idea, there should be an option for you to do that in the script. So to operate a bit on the structure of the tool. So you can think of the script as the movie the main movie composed of potentially multiple panels, where every panel is called a scene. And the scene is, you can think of it as a single molecule just to simplify. And the single molecule can have a list of actions so there are scripts that are composed of scenes and there are scenes composed of actions and actions are the most atomic thing. So the action would be something like rotation, like zoom, like animation, or some instantaneous thing like adding a label, you can have actions that are bundled together. And it happened at the same time, you're going to have actions that refer to external files to figures to data files to audio files, even to movies so you can have movies within movies, within movies, please don't do that. And there's a bunch of global options like frames per second like resolution that allow you to specify all those general properties of your movie, just in one place. And this will become clear as I show you some examples so this is just the abstract concept that I had in mind when writing the script that you don't need to really think of that in this terms. So what really happens is this is a Python script that is taking your input file, which is a text file, and it's translating the text file into a TCL script that gets interpreted by VMD. You might know if you're a VMD person that VMD has this TCL interface that allows you to do everything, that allows you to render things, automatically move things around and so on. And so the renders, the molecular renders from VMD are then augmented with all sorts of other graphics that you might want to use, be it external graphics or maybe just plus from Python or text from Python or maybe an external movie that would be incorporated into final movie. Then ImageMagic does all the processing, so composition, merging of files, conversion of formats, and this all in the end gets fed into FFmpeg along with any possible audio files to get you the final MP4 file. So from the user's perspective, this is just a TXT file being made into MP4. Again, you don't need to know all the things that happen. It might be helpful for you, but it's not an entry level requirement for sure. So we also tried to make installation easy so you can go with the regular PIP installation if you believe you have all the dependencies. Unfortunately, some of the dependencies are not part of Python. For instance, FFmpeg and VMD are not part of Python. So if you want to be safe and you're afraid you might miss some of the dependencies you might want to install through KONDAB. This will be more comprehensive. This will check all the dependencies and install them for you. Either in the existing virtual environment or in a new virtual environment, we have tutorials for that. So if you don't know what to choose, you can go to the website and check for you. And then we have tools to do sort of automatic setup. And we have this main command line called mollywood to run the script. We've tested that on Windows, Linux, and Mac. And it should work just fine. If you're a Windows person, I feel sympathetic, but eventually we made it work also for you so you can get it to run. It's never smooth on Windows, but well, that's just what it is. And now there's time for a short demonstration. So let me go to the terminal. I can run mollywood. If you run it just like this, it should tell you that you haven't provided an input. Normally you should run mollywood plus the name of the input, the text file. But if you want to generate a sample input, you can type I and it will generate something like sample mollywood input. The XT is something I use myself quite a lot because you can just take this file and modify it to suit your purpose. Then if you want to run a sample visualization just to show you, you can display only. So this doesn't render a movie. And you can see you have these things appearing here. Hopefully the playback is smooth in the stream. And that's it. In contrast, if you want to render it, you can type Y and then you can type render R. And it will do the same just much faster because it's only taking snapshots in the draft mode. And it will take literally 10 or 15 seconds until it's rendered. And then at the end, we should have the sample movie.mp4, which is literally the movie that we generated in, I would say, less than half a minute. So if you want to check that everything is running and works properly, you should be able to run this script in this manner. Okay, back to the presentation. So to show you actual movies that were generated in this way, here is a minimal example of an input. Well, it's not the minimal example because I could easily get rid of this line here. I just prefer to have the movie named in a custom way. What it says is, it says you will have a scene tbp, tbp stands for data binding protein. And the content of the scene will be a pdb with a code 1cw, which happens to be the data binding protein. And the list of actions for this scene will be zoom in by 1.4 over two seconds and then rotate around the y-axis by 360 degrees over two seconds. So that should be pretty intuitive. And if you look at that, that's exactly what happens. So this is literally the easiest thing to do, the most basic thing. And you should be able to get this running in again in a minute or less. You can see that the representation that we have here is sort of default, so it's new cartoon with the DNA without any colors and regular secondary structured coloring for the protein. So if you want to have something different, again the VMD people will recognize that you can go to VMD, you can add a bunch of representations, whatever you want. In this case, this would be like transparent water molecules, different colors for different parts of the protein to show the symmetry, licorice representation for the nucleic acid and so on. You can save that as a visualization state. And then this visualization state is something that you can put as a parameter here. And this will be used for the movie. And then you can do the same thing. And as you can see, the same thing is happening here, just with a different set of representations. If for whatever reason you want to make everything from scratch, so you don't want to touch VMD, you can still start with the PDB code. You can do some alignment in Mollywood, and you can remove, so make transparent default representation, and then you can recreate every single representation manually, so to say. So this is a selection, nucleic and no hydrogen using the licorice style, colored by type with a thickness of 1.5, so slightly secret and regular with the diffuse material and so on for the other materials. And so this does exactly the same thing as the VMD part. The point being, if you want to automatize things, for instance, if you want to do things on a cluster and so on, you can do that. This is along the lines of making complex things possible. So if you have a reason to do that, we just let you do that. We don't judge you. You know, you don't really need to understand everything that's going on in this slide. Just the point is that you can do many things from scratch in Mollywood. You don't need to be an expert in VMD, although it helps to know some, well, if you look at the documentation, it will be there. It still helps to know something about VMD. For sure. Then we have different types of actions. Some of the actions are instantaneous, meaning that they happen just in an instant. And some actions are finite time, which means they have some finite duration. If you look at the rotation here, this one doesn't really have any time, so it happens instantaneously. This one happens over two seconds, so this one should take longer. There are some actions that you can have both ways, so you can have them last some time or you can have them instantaneous. And there are some actions that are only one or the other. We have that again in the documentation, if you're curious. But the idea is that you can all do all sorts of jumps. You can do all sorts of initial setups and they won't be seen in the final movie. I know this is kind of obvious, but just to make the point, you can do that. So in the very beginning, I told you that the most general movie will be a grid of scenes. And if you want to have several scenes side by side, you can do that using the layout keyword when you specify the numbers of rows and columns, and then you specify the positions of every scene in that grid. And you can see that you basically have two things happening side by side in the same sequence of events with just different representations because I put different representations in those VMD files. The nice thing is that if you have two scenes that are identical in terms of the actions, you can define them in a single sequence like that. If you want them to be separate, you can do scene one list of actions and scene two list of actions, and this will be understood as well. Similarly, you can take the same two scenes and instead of showing them side by side, you can show them one after the other. And sometimes it might be useful in the old cinematic meaning of the word, scene where you have a scene and a cut and a scene and a cut and the movie just goes like that. So if you want to go more in the Hollywood direction, you can do a sequence of scenes. And the only thing you need to do is add this keyword, SC2 goes after SC1. So easy as that. Now one of the most important things in the script are the overlays. So the general concept of an overlay is just something that is being put on top of the movie. And by this I mean any sort of graphics, text, other movies and so on. And the simplest thing you can think of is putting another graphics as you can see here. So we're literally putting some PNG graphics at specified origin and with a specified size. We're also making the background transparent so that it doesn't occlude your molecule. There's sometimes a useful option to have. You can put any sort of text as well if you specify the location. Sometimes it requires a little bit of trial and error, but I will tell you later on how to streamline this to make it really fast. A more interactive kind of overlays would be the data overlay. And here you can see if you have an animation, so if you have a trajectory. You can have some sort of analysis associated with that trajectory. And so now you can actually plot the result of this analysis side by side with your movie or overlaid on top of your movie. And here if you have this overlay coupled with animation, you just need to provide a data file. Again the position, you can specify the aspect ratio if you want to have something more rectangular. And if you look closely, you can see that you can also put all sorts of equations and stuff generated with Lattec because we're plotting with Matlab. So all your Lattec comments should work if you want to put your e to the power of minus e over kbt equations in the labels. It should all work perfectly. So that is covered. There's also some flexibility in formatting of the curve. For instance you can specify the thickness, the color, the line style of the curve. Directly in the data file we have some keywords for that as well as the labels for the X and Y axis. So to go on, this is I think the most interesting and probably the most creative part where you can use other scenes as overlays. So what happens here is we basically have two scenes, but one of them is the base scene and one of them is laid on top of the other. I'm sorry for the moving rectangle. It doesn't, it just jumps back and forth. So what happens here in this moment, you can see we have an overlay that starts with an origin of 00 and a relative size of one, but then it goes to an origin of 0.065 and a relative size of 0.4. So you can have dynamically moving origin so you can move those overlays around. And this is a particularly nice trick, you know, just to take the sort of snapshot of some point in time and then move it to corner to make it like an inset with a zoom or with a different perspective or different molecular system or something like that. So again with that you can do many different interesting things I guess. And the last but, well, not last, not really last, but one of the things that you can do as well is you can add new representations on the fly. So you can see that we're adding all those license and arginine that are within that next to next to the DNA. So licorice representation, and then we want to modify their thickness so they can get bigger and then get smaller again. So we can dynamically modify their properties and then they can disappear. So you can you can have this mode down, which makes it hard to disappear. And the idea is that if you if you make a representation within alias and you can do many different things, just by referring the same alias so you can have many of these. You can have one representation one highlight and another highlight and so on and you can independently modify them over time, just as you as you want. And finally, we have this concept of overlapping or synchronous actions that you already know that you can have two actions happening at the same time. But you can also make them happen kind of synchronously so you can see this is rotation that is coupled with zoom and then translation that's coupled with rotation and the way we do that is the first half of the zoom is executed and then the second half of the zoom is coupled with with rotation. So this is basically a trick that allows you to split those things in into. And then the first half of the translation moves this thing away from the screen, and then you have this instantaneous movement back, and then you complete the second half of the translation. There's a whole bunch of nice tricks that you can use to make those things look things look nice and kind of cinematic again. So now, we have the documentation which is kind of extensive by by this point, and you can look at. We have the input structure we have a lot of comments on how to format your input. All sorts of things on how you can use the global parameters. There's a bunch of them and they're also well commented on. There's a list of actions at this time we have 17 different actions, I guess, and some of the actions are actually multifunctional so overlay you can have figures you can have data you can have movies you can have different things. So this is again very flexible every action has a list of defaults has a bunch of comments on how to use the parameters what the values mean. Are they relative or are they absolute should they be floating pointers or whatever. And we also have a bunch of issues so if you happen to see something that doesn't look right you can check with the list of known issues before you contact me. Obviously, there are more issues that are listed here but sometimes they're only dependent on you know, not really on the script but sometimes on on how things are set up in in the MD, or just the general limitations of the operation system. So this is the part is, I think, most educational, so to say, so we have a lot of minimal samples of movies, along with inputs. So let me just briefly show you some of these. For instance, this is one that shows you how to deal with. Whoops, sorry, how to deal with. Actually, this is the movie, how to deal with densities so you can change the ISO value for the density dynamically, you can overlay that with an atomistic model and things like that. And you have the code for that, and you have the comments on why things are this way. You're not alone if you want to learn to generate nice movies. This should help you a great deal. We have, I think every basic functionality covert now. So for instance here have a grid of movies that is automatically generated from automatically downloaded PDBs. If you want to make things like that, these are also quite simple. If you want to have something that has more than one molecule in the system, this is also feasible, you can freeze them and unfreeze them dynamically. Basically everything that's possible I only had the time to show so much in the in the webinar, maybe we will make a tutorial or a workshop movie in the future if there is any feedback for that. But for now I just wanted to show the basic capabilities we have much more obviously as you can, as you can see. And finally there is a bunch of teacher examples. These are long movies that really drive home the. Whoops. I cannot really show this in full screen I guess that really drives home the totality of what can be done with Molly sorry for the non full screen mode I don't know why this is zoomed in a bit. But you can see that we're actually combining a lot of functionalities here. You can see a nightmare to reproduce if you wanted to do that using homemade scripts and your own inventions that would take at least a week playing around with all the options. And that's another nice example with the QMM system here. And we're starting with an MD simulation of an MMS system that converts to a QM MD subsystem. And you have this nice. And transparency. Then you can look at two different pathways for two different reactions along with a free energy plot which is not really relevant now but let's just ignore that. And then you can have this sort of highlight of all the possible systems that were studied here. Putting one after one after another. So that's the sort of things that you can do when you want to play around with this tool long enough. And so I guess now you have an idea of how simple and how complex you can get just by playing around with the options. So we have this movie design workflow. This is one of the last things I want to show you. The idea being that there is an optimal seems to be an optimal workflow that you might want to follow if you want to create your movie in the fastest possible way. So first of all you can you can just ignore rendering you can just watch the things in VMD using one second long actions just to explore the parameters to see if you're rotating by the right amount of degrees if you're doing the right translations rotations and so on. Very quickly so you can iterate rapidly. Then you can start rendering in a draft mode which should take which should be very rapid again with something like FPS equals to so that you know you can place the overlays in in the right positions you don't spend too much time no rendering movie every time you want to change the placement of an overlay. And then you adjust the timings of all the actions and then you test everything in a draft mode with something like FPS 15 which should already be grand smooth. And you can set the final resolution and go to the full render turning off the draft mode with something like 25 frames per second which would be smooth enough. And well of course that can wait that can take several minutes maybe to several hours if you're if you have a very complex system in your movie is long enough. And then if you're not happy with that, you can still go to higher quality using this ambient occlusion which is a fancy setting for lightning in VMD that will again will take probably five times more time but the results will be spectacular. And so if you follow this this design really making a movie. Moderately advanced movie shouldn't take you more than an hour. I would say if you want to if you want to do something that is good enough for a conference talk. So summarizing all the key features that we have. We go from the text file to MP4 with no programming experience just following the examples and the syntax requirements. So, you know, knowing any of the tools that we use a VMD Python whatever is not necessarily an entry level requirement you can learn those things on the fly as you start trying more complex things. It should be easy to work with all sorts of numerical data with external graphics with audio with other movies. Audio might be useful. Particularly if you want to if you want to make educational movies for your whatever YouTube channel for the audience out there so you can put your voice over the movie. Whatever you really like. We can support this concurrent actions and asynchronous actions so if you want to have something more fancy or more complex than just action one of then action two action three, you can kind of intermingle them together. Just to make it give it a smoother vibe. Then we have a lot of flexibility in how you can treat the scenes so you can you can have scenes side by side you can have scenes one after the other can have one scene within another. Again you can be as creative as you want to. We have those dynamic representations that you can create you can destroy you can modify on the fly. Anything you want with all the possible representations in VMD that you want to use. One important feature I didn't mention yet is that if you want to, for instance, offload the rendering to an external workstation. You can easily, you know, take all the files that you use for the current project. Send them to a cluster or workstation far away and you can generate the movie without the graphical interface and just from the text interface just from the from the terminal. You can save you a lot of time if you have some, you know, powerful workstation out there, and you don't want to burn your CPU on your laptop. And last but not least we, we are open source and we remain free obviously we want to keep those options free because many. I can see that many tools are going commercial these days and Maya, for instance, is obviously commercial. The pie mall now is half commercial half free I don't know what the status is right now. But basically there are several things several tools that are only commercial and we wanted to have this counterbalance for for the people who don't like paying for for the software. So basically, in terms of the active intense development, I think we're done. I think we've put all the basic options that we wanted to put there. And now any future development is dependent on on your feedback. So if you think that we should have more actions if we should have more editable defaults, some parameters that will will be controlling different things. You should let us know we will think of that. Maybe we thought of that and discard the idea for some reason but maybe maybe we just didn't come up with with the idea because we didn't think of what you were thinking of doing. There was a question of supporting other softwares besides VMD. I was trying to make that work with Chimera which doesn't really work that well. I was looking into pie mall, which again. It's kind of fine but doesn't really follow the workflow that we do. So I eventually dropped this idea for now. I could go back to that if if anyone said, okay, I'm all would be super important for me and we need it. I think VMD for now is just sufficient. When it comes to the graphical interface, we had again we had discussions of whether we should have a graphical interface big but because we are relying on so many third party options. It will be kind of difficult to put those things together. So I think we're doing fine with the text interface, especially that you can do that remotely now we don't need to run this graphical tool. But if if many people tell us we should have a graphical interface, we can think of that. I think at this point it would only be viable as plug into VMD. But yeah, that's, I would say this and future now. And obviously we are doing ongoing debugging so if you find any errors and you check that these are not known issues. We will be happy to fix them if they are fixable within the script. And finally, we have the gallery that is still open to your examples. So if you think that you made something that is worth showing, you know, highlighting showing off. We can just email us and we can put your movie in the gallery if we if we think it's worth it. And with that I want to thank you for for the attention. We have this website that you can Google if you don't remember the name just remember to Google it with a single L. I think the double L Mollywood refers to a recent movie about some Los Angeles drug trafficking. I know our Mollywood is written with a single L. And they're also published. So if you like the tool. And if you use it for your paper, I remember to decide it. And with that, I am looking forward to questions. I think this is the moment to open the audience Q&A session. Thank you very much for the very interesting talk me wash. Really interesting way of doing visualization was fascinating. There's a number of questions. The first of which is from Super Chan. So the question is, is it possible to specify the vector of rotation option so that you can rotate along an axis instead of just X or Y or Z. I believe it was. I was considering at some point I think right now, the either is an option to rotate by some axis, it might be an option. Or there is an option to know simultaneously rotate around X and Y and Z, and you can get this final rotation as a combination of those. So for sure you can you can rotate off axis, if you're combining at least two axis. So this is possible. That's why you need to play around with with all those rapid iterations. Just to see, you know, which combination works for you. I know this is not ideal because it's hard to guess the rotation advance. And, well, this is something I was thinking about quite a lot, but I think in the end you have to you have to iterate to find the right combination. Great. Thank you very much. The next question we have is from Nisha. Nisha, I have unmuted your microphone. If you'd like to ask a question, please feel free to go ahead. Hi, yes. Very interesting dog. Love the app. So basically, the question was I use a lot of carbohydrate structures for protein carbohydrate interaction. Do you have any options for carbohydrates in particular? There's nothing specific to hydrocarbons, but if you use VMD to visualize carbohydrates using, I would say probably licorice, something similar to that. You can easily specify, you know, you can you have all the tools that are in VMD to specify your selection. And so I don't know if the carbohydrates selection or something similar works in general in VMD, but for sure you can customize it. Okay. Okay. So the carbohydrates, they specifically have SNFG format where you have different symbols, say for mannus, a sear, and then for Gluconac. So I think movies like that would be really helpful. You mean a different format of the file of the input file? No, no, the way of representation instead of having just the liquids. So you have a 3D structure like how we have for proteins. Yeah. I think I showed the example where you have the protein in like new cartoon and then you have DNA and licorice as this would be. Yes. Yes. And you can have all sorts of, you can have, you can have quick surface, you can have Van der Waals and other representations that are there in VMD. So you can again experiment with what works for you. Okay, thank you. Welcome. And thank you for the comment. Thank you very much for that answer. The next question we have is from Michael Brundel. Yeah, thank you for the talk. It's a very nice tool. Could you comment a bit more on how to include MD trajectory in the mollywood script and is this done in the mollywood script directly or with a VMD script? Yeah, sure. The, I think the most customizable thing, the most customizable way of doing that would be just to load the trajectory in VMD and save the visualization state it will be stored this way. You can also if you want to do that automatically can also specify PDB file and the trajectory in the input directly but then you will be dealing with the standards representation that you can again remove and replace with something you like. So this should be fairly easy. Okay, thank you. Welcome. Thank you. Thanks for that. The next question we have is from Bakari. Bakari asks, are there any integrations between mollywood with Jupyter notebook? Not really. So we tried to make it, we tried to make it command line only just to keep this simple functionality. But yet know how this would work. I mean, I can I can imagine you could you could have movies render in an individual individual boxes in the notebook. But we haven't really tried this. If, you know, there are enough people wanting to try this I can I can talk to the people here and we can we can think of maybe figuring this out. Interesting possibility, I guess. Thank you for the question. Thank you very much. So the next question, actually a small set of questions are from any cat. Yeah, thank you for the fantastic talk looks like an amazing app I had no idea about it. So really impressed. I have like three questions so I guess you answered some of them already but just to get sure so I'm interested in protein simulations movies and where in I want to fix the frame on a close up of a ligand. So if I get it right if I save the VMD file with the current state what I have to that will be taken further entering in the movie is that correct. So if you save the if you have the correct orientation in VMD and you save the other visualization state yeah this will be exactly started from this orientation so you can you can specify all the rotations in in advance. Or you can play with the settings and just find the one that works from you directly from from Hollywood but I think going through VMD would be easier. This is just for people who you know that some people's people who are not familiar with VMD so I prefer to have both options. Then you specified batch mode or with the without the GUI or without using the looking at the exact all the movies. So are there any examples of this like let's say I have like 30 trajectories of protein ligand complexes which are identical in composition so I just want to render 30 movies without looking at them what's happening every time. Yeah I was actually thinking that I never use that yet in real life but I was thinking that maybe if you have simulations on the cluster and you want to watch them. I can just you know instead of the only the trajectories you can generate the movies on the cluster. If the cluster of course allows you to install the tools with condo you can do that. If your cluster has an internal connection available to the users but that's that's a different story. Anyway the point is yeah the actual rendering if you're doing if you're doing draft rendering this is just done with snapshots or screenshots so you need to have a you need to have a display. But the tachyon rendering the high quality rendering is really done from the common line so you don't need to have the MD run with with a display. So you can absolutely run these things remotely. So is there an example in your on the website to do it and we take you on without open the opening of the GUI. Yes yes actually if you if you just if you just do draft mode equals false draft equals false which is the default it will by default run without the GUI. So just to run with the GUI you need to specify draft equals true you need to be in a draft mode. Okay and one last question without hogging too much time is it possible to get a gift instead of MP4. So far we haven't we haven't tried that I might explore that because maybe that would actually be easier for some people you know to pause on different different websites. Maybe there are also like simple and before to give connection conversion sorry websites that you can use but I realize it might be a nice feature to have right because I mean the idea is once we have a set of simulations we would like to put them on the slides directly from the Python without opening the PowerPoint and I think give might be easier so if you want looking for the feedback. Yeah that might be that might be interesting yeah right here right. Thank you. Thanks a lot once again. Yeah. Thank you. Thanks. The next question we have is from. Joe asks can you show in more details how one would do dynamic plotting. I imagine that there is an example on the website. Yeah there's plenty of examples if you want to you can you can even have to them two dimensional plots and you can have basically if you combine this overlay with an animation it will try to use the same frames from the data file that are used for the animation so it will be. It will be in unison. So the dot is moving on the plot just showing where the system is right now, but you can also customize it so if you want to give if you want to use different frames from the animation and different frames from the file you can also do that. And there's a bunch of options that you can explore. Everything is okay. I think we have like four or five examples. For the overlays themselves. For the overlays with data. Next question we have this from. Manav is asking what is the maximum time limit that a movie can have when done by mollywood and the maximum limit of what sorry could you repeat. Time that a movie. Time that is rendered through mollywood. I don't think there is a time limit. It can just take longer and I think that one limiting factor would might be disk space because you first render all the frames and then you compose all the frames but if you have sufficient disk space, it should be able to you know render as many as as you want. I made I never made movies longer than a minute though so. I don't see any potential issues with that but I also cannot say I tried to you know do super long movies. I was parsing movies with FM back that had several minutes so I know you can well there's no technical limits in this regard. I don't see any other issues that could arise maybe something would happen if someone tries to make you know to our movies and something like that but for any reasonable lengths that should be working. Thank you very much. Our penultimate set of questions are from Chitra and Chitra asks two quick questions the first one is is it possible to highlight amino acids within a movie. Yeah absolutely you you just put the highlight with name of a selection in the MD and if in the selection you specify the residue number of the name of the residue so if you say something like res name Allah it will highlight all the allanines if you say something like res name 45 it will highlight residue 45 so if you know what which amino acid you want to highlight it will do that and of course you can select the style. If you want to have it highlighted as a vulnerable surface or quick serve or liquories or whatever you can you can specify that. So quite easily. Thank you very much and our final question is from is from the question is the overlay of a pipeline graph on a movie is an excellent addition but does this support all pipeline options are only a select few. It's only a select few so we did a selection of the features that might be the most reasonable to have. And there's always a question of how we want to expand this I was thinking maybe of you know letting people write their own Python functions. But that would be already a complex function so until someone emails me with with a question like I want to do this and can this be done. I think we can stay with the set of options that we have if people need more flexibility we can we can expand this. We can also always try to you know there are some options that are you can specify the range in the X and Y direction. You can specify some simple options like the as I mentioned the the aspect ratio of the plots. But certainly not everything yeah that's that's a concern and I would I would at some point try to think of how to expand that if people want me to. Some great thank you very much and with that I'd like to take a moment to thank me wash again for talking about this very fascinating bit of software I mean quite honestly I wish this had been around when I was doing my PhD. But there you go. And I'd like to finish off by saying that there's there's a number of bio Excel webinars that happen quite regularly there's one coming up quite soon in just two weeks time which is going to be about using the guide training and professional development by Vera Masters and Malta sorry Marta Linaris. I hope that you can all come here come to see this because I think it will be a very interesting webinar and with that thank you again me wash and thank you everyone for coming here and for asking such great questions in the discussion. Thank you a lot also to the to all the people who asked the questions and to everyone who attended.