I am a medical doctor and I love using blender to teach intricate medical concepts to my students. I came across your channel recently. It helped me a lot in furthering up my CGI skills. Hats off.
Strange. I was trying this exact thing basically, but it exported weirdly and it indeed didn't show up in Avogadro. Knowing that it is possible makes a huge difference! Thanks again. I succeeded this time. Now I'll see if I can make an animation of the thing folding itself... **glup**
I've definitely found that sometimes it's a "try it three times" process, which can be frustrating. Animating them in any sensible way is a big challenge, but good luck! I mean, it's only protein folding right... not like it's a complicated problem or anything....
I want to make a Tobacco Mosaic Virus but when import the structure (3J06) in pyMoL software, only a single protomer is imported not a whole biological assembly as its visible on rcsb website. Could you please help me with this?
I don't actually use PyMol myself so I'm not as familiar with it. I know from the website that you can download the whole assemblies so you may have better luck just seeing if you can download the pdb directly from the database and then importing that. I was exploring that awhile ago for the Zika virus complex but ended up finding the file sizes too big for me to practically work with. You may also want to check out 3dproteinimaging which provides a service specifically for protein visualization.
Unfortunately I think this is more of an issue with how Avogadro generates the model and less the file format. In my experience with PyMOL I don't think you get the same seams between pieces. I do generally find .stl and .obj a bit more standard for many of the files I work with, I just haven't found a way to export from Avogadro using them.
@@CGFigures Yeah, I think Avogadro's exports are somewhat corrupted. Try exporting as .stl, .obj or .vrml from VMD or UCSF Chimera! and see if you get the same problems when importing in Blender. I haven't tried PyMol yet, I should also check that, thanks for reminding me its existence!
@@nazlidisalex I have Chimera but haven't had too much of a chance to play with it yet. Definitely something to check out though.... and this time I actually posted the comment from the right account....
Been playing around with this a bit now and I've noticed (as you mention in the video) that some protein pdb files have proteins in pairs. Are they paired in their respective organisms, or is there some other reason for this pairing?
Have you find a way to also export the colors of the protein instead of adding one single shader to the whole structure? At the moment I can only do that with Jmol using the obj format, which is accompanied with a .mtl file containing the color information
I haven't found a way to do that yet, but I also tend to prefer shading in Blender. The only time I try to preserve colour data is if I have many discrete objects like individual atoms
Hi Abir, if you select specific faces and then run tris to quads it should only change the selected faces leaving the remaining unselected ones as tris.
That's a new one. If you're getting the .pdb from Avogadro the first thing I recommend is trying to access/create it through the protein databank database or through another program like pymol or ChimeraX. In my experience the issue is usually the underlying pdb file being written with coordinates that don't make sense.
I'm pretty sure my hardware has the horsepower for larger molecules. However, whenever I try to import "myosin" or "tubulin", I don't get any result. Do you know why that might be? Great tutorials! Thanks so much for these. :)
If you don't mind sharing your hardware specs that would be helpful (I am also trying to figure out the limits of the approach). Another question though is where does the import fail? In Avogadro or in Blender? If it's failing in Avogadro you might be able to get the .wrl from PyMOL, Chimera or 3DProteinImaging. If it's failing in Blender then you might have better luck with a .stl or .obj which Alex has mentioned you can get from Chimera
@@CGFigures I have a 4GHz CPU, 64 gigabytes of RAM, and two Video cards running in parallel. I'd rather doubt it's a processing issue, as my recently upgraded system has been able to handle everything I've been able to throw at it so far. I'll try those other approaches you mentioned. Thanks. :)
I am a medical doctor and I love using blender to teach intricate medical concepts to my students. I came across your channel recently. It helped me a lot in furthering up my CGI skills. Hats off.
Strange. I was trying this exact thing basically, but it exported weirdly and it indeed didn't show up in Avogadro. Knowing that it is possible makes a huge difference! Thanks again. I succeeded this time. Now I'll see if I can make an animation of the thing folding itself... **glup**
I've definitely found that sometimes it's a "try it three times" process, which can be frustrating. Animating them in any sensible way is a big challenge, but good luck! I mean, it's only protein folding right... not like it's a complicated problem or anything....
Amazing! I wonder how to achieve the rendering effect of the cover image，could you please give me some idea?
I want to make a Tobacco Mosaic Virus but when import the structure (3J06) in pyMoL software, only a single protomer is imported not a whole biological assembly as its visible on rcsb website. Could you please help me with this?
I don't actually use PyMol myself so I'm not as familiar with it. I know from the website that you can download the whole assemblies so you may have better luck just seeing if you can download the pdb directly from the database and then importing that. I was exploring that awhile ago for the Zika virus complex but ended up finding the file sizes too big for me to practically work with. You may also want to check out 3dproteinimaging which provides a service specifically for protein visualization.
Great tutorials! I wonder if you get the same topology problems if you export proteins from VMD as .stl or .obj. Thanks for sharing!
Unfortunately I think this is more of an issue with how Avogadro generates the model and less the file format. In my experience with PyMOL I don't think you get the same seams between pieces. I do generally find .stl and .obj a bit more standard for many of the files I work with, I just haven't found a way to export from Avogadro using them.
@@CGFigures Yeah, I think Avogadro's exports are somewhat corrupted. Try exporting as .stl, .obj or .vrml from VMD or UCSF Chimera! and see if you get the same problems when importing in Blender. I haven't tried PyMol yet, I should also check that, thanks for reminding me its existence!
@@nazlidisalex I have Chimera but haven't had too much of a chance to play with it yet. Definitely something to check out though.... and this time I actually posted the comment from the right account....
Been playing around with this a bit now and I've noticed (as you mention in the video) that some protein pdb files have proteins in pairs. Are they paired in their respective organisms, or is there some other reason for this pairing?
That was fast... haha great!
Thanks a lot!
Have you find a way to also export the colors of the protein instead of adding one single shader to the whole structure? At the moment I can only do that with Jmol using the obj format, which is accompanied with a .mtl file containing the color information
I haven't found a way to do that yet, but I also tend to prefer shading in Blender. The only time I try to preserve colour data is if I have many discrete objects like individual atoms
Protein Imager exports mesh in vrml2 format with colours on vertices :)
How to convert some but not all the triangles to quads?
Hi Abir, if you select specific faces and then run tris to quads it should only change the selected faces leaving the remaining unselected ones as tris.
when i try to import the pdb file I get this error, " Specified molecule could not be loaded: 1crn.pdb"... what do I do?
That's a new one. If you're getting the .pdb from Avogadro the first thing I recommend is trying to access/create it through the protein databank database or through another program like pymol or ChimeraX. In my experience the issue is usually the underlying pdb file being written with coordinates that don't make sense.
I'm pretty sure my hardware has the horsepower for larger molecules. However, whenever I try to import "myosin" or "tubulin", I don't get any result. Do you know why that might be?
Great tutorials! Thanks so much for these. :)
If you don't mind sharing your hardware specs that would be helpful (I am also trying to figure out the limits of the approach). Another question though is where does the import fail? In Avogadro or in Blender? If it's failing in Avogadro you might be able to get the .wrl from PyMOL, Chimera or 3DProteinImaging. If it's failing in Blender then you might have better luck with a .stl or .obj which Alex has mentioned you can get from Chimera
@@CGFigures I have a 4GHz CPU, 64 gigabytes of RAM, and two Video cards running in parallel. I'd rather doubt it's a processing issue, as my recently upgraded system has been able to handle everything I've been able to throw at it so far.
I'll try those other approaches you mentioned. Thanks. :)
@@Starbat88 Fair enough. Sounds like your build is an absolute beast. Thanks for sharing.