you really helped me thanks a lot . i am so strugglled to get the exact atomic structure of silicon finally i did it. thank you. and dont stop this kind of educational videos
Important time stams for revision 4:10 Activate atomic blender add-on 5:35 controlling bond shape with object data properties 8:15 Making atom instances real
Thank you for your tutorial. It is easily understandable and extremely interesting. I am wondering how to add polyhedral in the crystal structures. Eg: make Sulphur tetragonal for Zn in this case. Thanks!
@@CGFigures Thank you for your reply. I mean one Zn atom bonds with 4 S atoms, so Zn is inside a tetragonal of 4 S. In other softwares like Avocado, or Vesta, I can choose styles to demonstrate the crystal structure like 'Ball and stick', 'Stick', or 'polyhedral'. In your tutorial, you show how to modify stick and ball style (the size and color of atoms and the bonding among atoms). My query is how to add a polyhedral style (tetragonal or octahedral) in this tutorial. I hope you get my point. Thanks again!
@@manhxuanpham7832 I think I follow. It's a bit of an interesting problem. I'm not immediately sure how to do it in avogadro or vesta. There might be an easy workaround where you select all the points related to one type of atom and just hit "F" to make faces. There's no guarantee that would work and up until now I've made custom nodes or assets when I make a lattice that has polyhedra (perovskites or lithium cobalt oxide). I'll give this a look and see if I can get to a better general solution.
@@CGFigures I also watched the video which you instruct how to make perovskites and lithium cobalt oxide. So I will follow it to make tetrahedrals for the cystal structure and wait for a better general solution.
I haven't worked with VESTA personally, but I find that so long as you get the same file format these approaches tend to work, even if they aren't as good as they could be. I've used Chimera, Avogadro, PyMol, molview, Chem3D, most work.
Thanks for making these videos! In my experience, VESTA crashes far less than Avogadro and can handle larger numbers of atoms. The clipping issue that Avogadro had in this video would likely be avoided with VESTA.
It's been two years since this video was released. But now with 3.4, you showed your TMD and graphene assets in one of your latest videos (B & S - ep 3) which showed far greater semi-auto tunability than this one or your LiCoO video. So could you please make another tut of this video (using TMD) showing your latest workflow with such tunability? It'd be really helpful! Thanks!
Hey Abdullah. Short version: If I can I will make a more blender-based tool for working with crystal data. I haven't done that yet. Long version: Each of the things you mentioned are a little different. The LiCoO is very old and just a rough visual approximation using admittedly older (and kind of outdated) tools. This video uses actual data and there are times where that is really valuable. I don't have a good replacement for that yet. It might be something that gets done in 2023. The TMD and graphene assets are all based on geonodes and are also just visual approximations but there isn't really a workflow to present. Those assets are much more of a "build it and let people use it" than a "create a tutorial and have people adapt it" kind of situation.
@@CGFigures Thanks for the reply, and this totally makes sense! I think, in some of these grey-area cases, even your rough workflow (as opposed to a polished tutorial) can be a great help for the community, as there's literally nothing of this sort on the internet at the moment (to the best of my knowledge)!
It should be possible. If you join the whole crystal into one object with Ctrl+J you could try to apply a simple deform directly. You could also use a lattice/lattice modifier. It's a bit of a rough approach but I have used it in the past with perovskites.
0:14 It’s a standard package in the Debian repository, so those running Debian and derivatives can just install it from their package manager. Hmm, it appears the Debian package does not include .cif support.
MKJB's suggestion is a cool place to start for sure. I've done a bit of exploring with surfaces and "On Growth and Form" is on my reading list so I'll definitely give this one a look.
@@coreys2686 You welcome! ;) There is an our math and real matma (in Polish and Sanskrit same word...). Real shell of real snail and nautilus are much more beautiful (complex) geometry than we can calculate. First, these structures are free. We always try to get the so-called a strictly defined result, and there is no such thing. Fortunately, quantum computers will soon appear, and they will help us to highlight the obvious - that everything is a beautifully organized chaos. Either way, of course it is worth studying all these matters at any stage. Btw - Please, try to find information, how nautilus is not compatible with the golden ratio... Memes are wrong ;) Of course it does but in more sophisticated way...
@@CGFigures Good and the most beautiful direction is also L-system... and Tissue... ;) I love these topics... They are more powerful than we think... :) Please take a look - I used algae as photoactive material... (I am sorry, this is in Polish but translator is not so bad...): quantumidea.tech/2019/08/08/stwarzarka-organiczna/ quantumidea.tech/2020/06/07/wszystko-jest-informacja-informacja-jest-wszystkim/
Very possibly an option though I'm trying to move towards a few alternatives such as PyMol and Chimera for the future as I think they offer a bit more functionality more readily.
Thank you for this awesome video. I have a question, I want to use draw the polygons in my crystal cif file. However, each time I import the file into blender, it becomes the ball and stick, do you know how I can turn them to the polygon in the original file in avogadro？ Thank you！
I'm sorry to say I don't have an easy fix for this. I haven't spent much time in Avogadro lately and I find it can be a bit fiddly. It's an excellent question though, so I might revisit this... I've had a number of questions about MOFs that would make it very worthwhile.
If you use Ctrl+A to realize the instances then you should be able to select the individual atoms (try using L in edit mode). Once you have the atom you want selected you can add a unique material to it. Just be careful about using this for large crystals though, making the instances real takes up a lot more computer power so I wouldn't recommend it for very large crystals
Question, what are the specs of the pc you are workin on? I am mostly curious about RAM capacity and processor speed. I wanna try this but i am scared of any 3D projects, i dont want my laptop to crash XD
I've worked with a bunch of machines over the years. My main PC right now has 64 gb of 3200 DDR4 RAM (originally 32), and a Ryzen 5 3600. I started out doing Blender work on a Toshiba laptop from 2009 and my older desktop was a XPS 8700 that had... 16 gb of ram (DDR3) and a i7-4790. Bigger crystals can definitely be a problem for lighter hardware. Newer versions of Blender are also much more efficient though and are pretty friendly. If you're having a really hard time it might be better to try to use a cloud computing option if that is possible. I believe Josh Gambrell has some older videos discussing those options.
If I choose say the same setting for a molecule rather than a crystal, would I get similar results? Another question: How can I convert a measured crystal into a PDB file? I tried to open my CIf file with Avogadro but it failed! Many thanks in advance.
The same Blender settings will work for molecules. I have a separate video on the channel that covers molecules and the workflow is quite similar. I'm not a crystallographer myself so I'm not sure I can help you with the second part. I'm assuming you mean that you acquired the .cif file from an actual crystal structure. I've seen some online forums suggest either Mercury or OpenBabel to convert .cif to .pdb. I haven't used Mercury but I've had decent luck with OpenBabel. Hope that helps.
Green... That's interesting. If you had said purple I'd would have guessed that Blender was missing a file for the lighting or for a texture. What kind of materials do you have applied to the atoms? This might be a problem with the normals being flipped
Working on some graphics for an ACS journal - this stuff is a gold mine! Thanks so much!!!
Your channel is pure treasure. I'm so happy that I found you today and subscribed. Keep up the good work! Thank you!
you really helped me thanks a lot . i am so strugglled to get the exact atomic structure of silicon finally i did it. thank you. and dont stop this kind of educational videos
I love your tutorials so much! After finishing my master thesis I'll follow them one by one, they're amazing! Thank you for doing this!
That is incurable .. many thanks for sharing
Thanks for very interesting tutorials. This is exactly what I was looking for 🙂
Important time stams for revision
4:10 Activate atomic blender add-on
5:35 controlling bond shape with object data properties
8:15 Making atom instances real
Hello Joe! A lot of thanks for the useful content!
Thank you so much
Thanks a lot. Helpful tutorials
Excellent/ Thanks
Thank you for your tutorial. It is easily understandable and extremely interesting. I am wondering how to add polyhedral in the crystal structures. Eg: make Sulphur tetragonal for Zn in this case. Thanks!
Hi Manh, I'm not sure I understand your question. Can you provide an example?
@@CGFigures Thank you for your reply. I mean one Zn atom bonds with 4 S atoms, so Zn is inside a tetragonal of 4 S. In other softwares like Avocado, or Vesta, I can choose styles to demonstrate the crystal structure like 'Ball and stick', 'Stick', or 'polyhedral'. In your tutorial, you show how to modify stick and ball style (the size and color of atoms and the bonding among atoms). My query is how to add a polyhedral style (tetragonal or octahedral) in this tutorial. I hope you get my point. Thanks again!
@@manhxuanpham7832 I think I follow. It's a bit of an interesting problem. I'm not immediately sure how to do it in avogadro or vesta. There might be an easy workaround where you select all the points related to one type of atom and just hit "F" to make faces. There's no guarantee that would work and up until now I've made custom nodes or assets when I make a lattice that has polyhedra (perovskites or lithium cobalt oxide). I'll give this a look and see if I can get to a better general solution.
@@CGFigures I also watched the video which you instruct how to make perovskites and lithium cobalt oxide. So I will follow it to make tetrahedrals for the cystal structure and wait for a better general solution.
Wouldnt some of the issues with avogadro be avoided by using VESTA instead?
I haven't worked with VESTA personally, but I find that so long as you get the same file format these approaches tend to work, even if they aren't as good as they could be. I've used Chimera, Avogadro, PyMol, molview, Chem3D, most work.
Thanks for making these videos! In my experience, VESTA crashes far less than Avogadro and can handle larger numbers of atoms. The clipping issue that Avogadro had in this video would likely be avoided with VESTA.
It's been two years since this video was released. But now with 3.4, you showed your TMD and graphene assets in one of your latest videos (B & S - ep 3) which showed far greater semi-auto tunability than this one or your LiCoO video. So could you please make another tut of this video (using TMD) showing your latest workflow with such tunability? It'd be really helpful! Thanks!
Hey Abdullah.
Short version: If I can I will make a more blender-based tool for working with crystal data. I haven't done that yet.
Long version: Each of the things you mentioned are a little different. The LiCoO is very old and just a rough visual approximation using admittedly older (and kind of outdated) tools. This video uses actual data and there are times where that is really valuable. I don't have a good replacement for that yet. It might be something that gets done in 2023. The TMD and graphene assets are all based on geonodes and are also just visual approximations but there isn't really a workflow to present. Those assets are much more of a "build it and let people use it" than a "create a tutorial and have people adapt it" kind of situation.
@@CGFigures Thanks for the reply, and this totally makes sense! I think, in some of these grey-area cases, even your rough workflow (as opposed to a polished tutorial) can be a great help for the community, as there's literally nothing of this sort on the internet at the moment (to the best of my knowledge)!
This is amazing! I am just wondering if it is possible to bend these crystal structures?
It should be possible. If you join the whole crystal into one object with Ctrl+J you could try to apply a simple deform directly. You could also use a lattice/lattice modifier. It's a bit of a rough approach but I have used it in the past with perovskites.
0:14 It’s a standard package in the Debian repository, so those running Debian and derivatives can just install it from their package manager.
Hmm, it appears the Debian package does not include .cif support.
Great subject as usual.
Any idea how to make a snail shell or nautilus shell?
I've tried in the past, but I've been trying the wrong stuff.
Add -> Mesh -> Math Function -> XYZ Math Surface
MKJB's suggestion is a cool place to start for sure. I've done a bit of exploring with surfaces and "On Growth and Form" is on my reading list so I'll definitely give this one a look.
@@mkjb8331 thanks for that. I guess I need to learn some math to change the shape.
Is there formulae for the shape of a shell?
@@coreys2686 You welcome! ;) There is an our math and real matma (in Polish and Sanskrit same word...). Real shell of real snail and nautilus are much more beautiful (complex) geometry than we can calculate. First, these structures are free. We always try to get the so-called a strictly defined result, and there is no such thing. Fortunately, quantum computers will soon appear, and they will help us to highlight the obvious - that everything is a beautifully organized chaos.
Either way, of course it is worth studying all these matters at any stage.
Btw - Please, try to find information, how nautilus is not compatible with the golden ratio... Memes are wrong ;) Of course it does but in more sophisticated way...
@@CGFigures Good and the most beautiful direction is also L-system... and Tissue... ;)
I love these topics... They are more powerful than we think... :)
Please take a look - I used algae as photoactive material... (I am sorry, this is in Polish but translator is not so bad...):
quantumidea.tech/2019/08/08/stwarzarka-organiczna/
quantumidea.tech/2020/06/07/wszystko-jest-informacja-informacja-jest-wszystkim/
wow.........
2:44 How about changing the view projection from Perspective to Orthographic.
Very possibly an option though I'm trying to move towards a few alternatives such as PyMol and Chimera for the future as I think they offer a bit more functionality more readily.
Thank you for this awesome video. I have a question, I want to use draw the polygons in my crystal cif file. However, each time I import the file into blender, it becomes the ball and stick, do you know how I can turn them to the polygon in the original file in avogadro？ Thank you！
I'm sorry to say I don't have an easy fix for this. I haven't spent much time in Avogadro lately and I find it can be a bit fiddly. It's an excellent question though, so I might revisit this... I've had a number of questions about MOFs that would make it very worthwhile.
Can you please tell of how could I change the colour of a particular atom only and not all together? Thanks.
If you use Ctrl+A to realize the instances then you should be able to select the individual atoms (try using L in edit mode). Once you have the atom you want selected you can add a unique material to it. Just be careful about using this for large crystals though, making the instances real takes up a lot more computer power so I wouldn't recommend it for very large crystals
Question, what are the specs of the pc you are workin on? I am mostly curious about RAM capacity and processor speed. I wanna try this but i am scared of any 3D projects, i dont want my laptop to crash XD
I've worked with a bunch of machines over the years. My main PC right now has 64 gb of 3200 DDR4 RAM (originally 32), and a Ryzen 5 3600. I started out doing Blender work on a Toshiba laptop from 2009 and my older desktop was a XPS 8700 that had... 16 gb of ram (DDR3) and a i7-4790. Bigger crystals can definitely be a problem for lighter hardware. Newer versions of Blender are also much more efficient though and are pretty friendly. If you're having a really hard time it might be better to try to use a cloud computing option if that is possible. I believe Josh Gambrell has some older videos discussing those options.
If I choose say the same setting for a molecule rather than a crystal, would I get similar results? Another question: How can I convert a measured crystal into a PDB file? I tried to open my CIf file with Avogadro but it failed! Many thanks in advance.
The same Blender settings will work for molecules. I have a separate video on the channel that covers molecules and the workflow is quite similar. I'm not a crystallographer myself so I'm not sure I can help you with the second part. I'm assuming you mean that you acquired the .cif file from an actual crystal structure. I've seen some online forums suggest either Mercury or OpenBabel to convert .cif to .pdb. I haven't used Mercury but I've had decent luck with OpenBabel. Hope that helps.
Hi, when i try to render, everything changes to green. What might be the issue.
Green... That's interesting. If you had said purple I'd would have guessed that Blender was missing a file for the lighting or for a texture. What kind of materials do you have applied to the atoms? This might be a problem with the normals being flipped
Please post a video on how to make chrystal meth in my kitchen blender... with only free assets!