Double bonds can be a bit tricky. Make sure you have the "bonds" box checked in Blender, otherwise it will only show single bonds. Sometimes this is a problem with the pdb file. In open babel try checking the box for "Generate 3D coordinates" and then converting. This is covered in the original version of the tutorial if you need a bit more reference.
mhI just saw the other video and I already tried everything, I want to generate the TNT molecule, I frame the 3D box, and I save but the molecule that blender imports now looks crooked, I don't know if it's because it's a small molecule or because the resonance of the nitro groups
I just tried to generate the same molecule that you see here (antrhacene) but the same thing happens to me, I can't generate the double bonds and when framing the 3d box the molecule looks horrible.
At 3:40, after amking instances real, you say Shit and J to select any atom, but I think it is only Shift and then selection, after that Ctrl+J to join.
I would love to see how you would make cyclodextrins, or something that can be easily and quickly scaled up or down depending on how many repeating units it has. I think CDs would be a cool problem since it has a conical shape and can have changing amounts of glucose molecules, altering the radius.
Polymers in general are something I've wanted to tackle for awhile. There are definitely some tricks to them on the implementation side. Years ago I was involved with a project making cyclic polymers and it would be very cool to add that as a toggle option to a general tool.
This is something I've been meaning to look at it in more detail. Entropic has a great tutorial on making stylized p-orbitals though if you're looking for a place to start. czcams.com/video/sz7hYOclmvc/video.html&ab_channel=Entropic
Thanks for the great tutorial. I’m wondering how I can change the bonds color. I mean a same color for all of the bonds which is different from atoms. Thanks
I believe the longer version of this tutorial covers how to separate the materials for the bonds vs the atoms just around the 19 minute mark. It is linked in this video's description
Hey there. Could you clarify what you mean by expand the structure range? If you're asking about larger molecules I would recommend looking into Molecular Nodes.
If you're doing your minimization in Avogadro I believe the .mol format will preserve the geometry it takes on when you save the file. From there it should just be following the rest of the process.
How can I import the Space Filling model to Blender? Does it have something to do with Babel? There is a space filing option in the importing menu however it keeps on giving me ball and stick model.
You can create the look of a space filling model by just making all the atom sizes larger. You can also export VRML formats from Avogadro (and I think from ChimeraX) but working with those is a little different. I detail a bit of that workflow in my tutorial on making proteins (czcams.com/video/H4eT5FFX7lU/video.html&ab_channel=CGFigures)
is there any way to model sigma or pi bonds? Im doing a project for school and I'm having a bit of trouble trying to model those using blender and this website.
Hey abbie, I gather you're referring to the isosurface representations. If I've got that right you might want to try following along with this blog post from the Hartley group website blog.hartleygroup.org/2016/02/22/visualizing-molecular-isosurfaces-mos-etc-in-blender/
Hello ! Thanks very much for this tutorial. Unfortunately, this doesn't work for me ... i have this error message when trying to import my .pdb file into Blender. Python : Traceback (most recent call last): File "C:\Program Files\Blender Foundation\Blender 3.4\3.4\scripts\addons\io_mesh_atomic\pdb_gui.py", line 198, in execute import_pdb(self.ball, File "C:\Program Files\Blender Foundation\Blender 3.4\3.4\scripts\addons\io_mesh_atomic\pdb_import.py", line 1335, in import_pdb mat_P_BSDF = material.node_tree.nodes['Principled BSDF'] KeyError: 'bpy_prop_collection[key]: key "Principled BSDF" not found' Do you know why this doesn't work ? Thanks by advance
This one is interesting. Haven't seen that before. What molecule are you trying to represent? Usually the issues I find people encounter are with not having atomic blender installed or with using NURBS instead of Mesh for the ball import settings. I get the feeling this might be an issue with your molecule though. Possibly if it has some strange heteroatoms. Otherwise it's not an error I've seen. I would suggest trying a different molecule or another version of Blender.
Hello, I had the same problem and I just had to change the input format to ''mol - - MDL MOL format'' (its in the upper left corner) I hope this helps! :)
I've managed to get this to work in version 3.2 and 3.3. Multiple bonds can be tricky. I've pinned a comment that works through some troubleshooting options.
Hello its amazing but i have a problem, in my case the double bonds are not generated any suggestion?
Double bonds can be a bit tricky. Make sure you have the "bonds" box checked in Blender, otherwise it will only show single bonds. Sometimes this is a problem with the pdb file. In open babel try checking the box for "Generate 3D coordinates" and then converting. This is covered in the original version of the tutorial if you need a bit more reference.
mhI just saw the other video and I already tried everything, I want to generate the TNT molecule, I frame the 3D box, and I save but the molecule that blender imports now looks crooked, I don't know if it's because it's a small molecule or because the resonance of the nitro groups
I just tried to generate the same molecule that you see here (antrhacene) but the same thing happens to me, I can't generate the double bonds and when framing the 3d box the molecule looks horrible.
well i find this resolution
m.czcams.com/video/YNoow7qkwFA/video.html
@@lunacy_vicius did you solve it? im having the same issues
Holy moly this is a great video. It's even easier to create visualizations with your Blender tutorials than using VMD haha
I've been sharing this with my colleagues 😀
Great malecus. So useful video thank you
At 3:40, after amking instances real, you say Shit and J to select any atom, but I think it is only Shift and then selection, after that Ctrl+J to join.
Great video
I would love to see how you would make cyclodextrins, or something that can be easily and quickly scaled up or down depending on how many repeating units it has. I think CDs would be a cool problem since it has a conical shape and can have changing amounts of glucose molecules, altering the radius.
Polymers in general are something I've wanted to tackle for awhile. There are definitely some tricks to them on the implementation side. Years ago I was involved with a project making cyclic polymers and it would be very cool to add that as a toggle option to a general tool.
Nice work. Always helped me.thanks
Thanks for sharing!
I'm not a scientist but I had to design a molecule graphic for a campaign. This was SO HELPFUL, thanks!!!!
Thank you so much.
Thanks for another great video. Can you please do a video on how to animate Atomic Orbital Hybridization in blender, e.g. sp³, sp², sp in carbon?
This is something I've been meaning to look at it in more detail. Entropic has a great tutorial on making stylized p-orbitals though if you're looking for a place to start. czcams.com/video/sz7hYOclmvc/video.html&ab_channel=Entropic
Thanks for the great tutorial. I’m wondering how I can change the bonds color. I mean a same color for all of the bonds which is different from atoms. Thanks
I believe the longer version of this tutorial covers how to separate the materials for the bonds vs the atoms just around the 19 minute mark. It is linked in this video's description
Thanks for your nice job. How to freely expand the structure range?
Hey there. Could you clarify what you mean by expand the structure range? If you're asking about larger molecules I would recommend looking into Molecular Nodes.
How can I import molecule with not flat structure after energy minimalization?
If you're doing your minimization in Avogadro I believe the .mol format will preserve the geometry it takes on when you save the file. From there it should just be following the rest of the process.
Double bounds are not supported in pdb format so in blender appear as single bonds
How did you fix this problem?
Generate 3D coordinate does not work😢
Unfortunately I believe this is a version problem. It's been one of the more consistently commented issues and I haven't found a clear solution yet.
How can I import the Space Filling model to Blender? Does it have something to do with Babel? There is a space filing option in the importing menu however it keeps on giving me ball and stick model.
You can create the look of a space filling model by just making all the atom sizes larger. You can also export VRML formats from Avogadro (and I think from ChimeraX) but working with those is a little different. I detail a bit of that workflow in my tutorial on making proteins (czcams.com/video/H4eT5FFX7lU/video.html&ab_channel=CGFigures)
Could you make tutorials about lab equipment such as hot plates, mechanical stirrers, and phototelectrochemical cells, etc...
is there any way to model sigma or pi bonds? Im doing a project for school and I'm having a bit of trouble trying to model those using blender and this website.
Hey abbie, I gather you're referring to the isosurface representations. If I've got that right you might want to try following along with this blog post from the Hartley group website blog.hartleygroup.org/2016/02/22/visualizing-molecular-isosurfaces-mos-etc-in-blender/
@@CGFigures Thank you so much! That’s exactly what I was looking for :)
I really need to know how to save the work as a png, if there is a video u hvae mentioned this in it, please let me know what it is
This is available once you have rendered the image. There are options to save as a png.
@@CGFigures yes, but still the background is not transparent
Hello ! Thanks very much for this tutorial. Unfortunately, this doesn't work for me ... i have this error message when trying to import my .pdb file into Blender.
Python : Traceback (most recent call last):
File "C:\Program Files\Blender Foundation\Blender 3.4\3.4\scripts\addons\io_mesh_atomic\pdb_gui.py", line 198, in execute
import_pdb(self.ball,
File "C:\Program Files\Blender Foundation\Blender 3.4\3.4\scripts\addons\io_mesh_atomic\pdb_import.py", line 1335, in import_pdb
mat_P_BSDF = material.node_tree.nodes['Principled BSDF']
KeyError: 'bpy_prop_collection[key]: key "Principled BSDF" not found'
Do you know why this doesn't work ?
Thanks by advance
This one is interesting. Haven't seen that before. What molecule are you trying to represent?
Usually the issues I find people encounter are with not having atomic blender installed or with using NURBS instead of Mesh for the ball import settings. I get the feeling this might be an issue with your molecule though. Possibly if it has some strange heteroatoms. Otherwise it's not an error I've seen. I would suggest trying a different molecule or another version of Blender.
Hello, I had the same problem and I just had to change the input format to ''mol - - MDL MOL format'' (its in the upper left corner) I hope this helps! :)
The latest version of blender doesn't provide double bond......
I've managed to get this to work in version 3.2 and 3.3. Multiple bonds can be tricky. I've pinned a comment that works through some troubleshooting options.
how to setup and download open babel?
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The longer version of this video walks through installation of open babel and is linked in the description of this video
😁 ｐｒｏｍｏｓｍ
So it's basically just the same thing you post over and over and over again...
I do like consistency. But if there are suggestions for new science-related blender topics I do keep a running list open.