of course! Thank you!
Very good! However, here is a version, where the size and materials of the elements are conserved, have a look.
Cheers.
pdb_import.py (66.6 KB)
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Hey @Blendphys,
I’m starting slowly to work on my protein, sorry being late to get any update. I got stuck at the PDB loading step, somehow I got such a strange scene after loading my PDB, each atom is showing as cubic instead of spherical shape. I also tried another file from Protein Data Bank but still showing the same.
Hello,
I’ve been running into some issues with getting double bonds to show up when importing a .PDB file. I’ve tried quite a few different converters, manually changing files, etc, and I can’t seem to figure out what I’m doing wrong. The syntax in the plugin seems pretty simple when it comes to parsing this so I’m not sure what I’m misunderstanding.
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.90
HETATM 1 C UNL 1 -10.284 -3.608 0.000 1.00 0.00 C
HETATM 2 O UNL 1 -10.229 -4.826 0.000 1.00 0.00 O
CONECT 1 2 2
CONECT 2 1 1
MASTER 0 0 0 0 0 0 0 0 2 0 2 0
END
Here’s an example file that should have a single double bond. I run into this issue with “Simple” and “Dupliverts” import setting. I haven’t been able to get one double bond to appear.
Is there a converter that would be recommended for ensuring the format is correct? I’m trying to go from a .mol to a .pdb with bonds preserved.
Hi Ezra_Hill.
Take and study this example here, it is a CO2 molecule and it works:
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 -3.327 0.976 0.009 1.00 0.00 C
HETATM 2 O LIG 1 -2.208 0.553 0.042 1.00 0.00 O
HETATM 3 O LIG 1 -4.445 1.400 -0.025 1.00 0.00 O
CONECT 1 2 2 3 3
CONECT 2 1 1
CONECT 3 1 1
MASTER 0 0 0 0 0 0 0 0 3 0 3 0
END
I hope, it helps … . Cheers.
PS: I’m currently almost unavailable … this is the reason why it takes so long with my answers, sry. 
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Hi wenchangyu2006!
Strange, it seems that the representative ball of a instancing vertex structure is not represented at all the vertices. This is the reason why you see all these dots (vertices) in the viewer.
Which patch file are you using? Can yo give us also the PDB file, plz?
Cheers.
PS: I’m currently almost unavailable … this is the reason why it takes so long with my answers, sry.
@Blendphys thanks for getting back, no worries if you don’t have time.
Regarding the patch file, I use your latest one where the size and materials of the elements are conserved.
My PDB is here, https://www.dropbox.com/s/9ojwh5dnyhd5vvu/noh.pdb?dl=0
Thanks!
very strange, here your file works!
Which Blender version are you using? I use a self-compiled Ubuntu 20.04 Blender 3.2.0 Alpha version … .
oh that is strange, I have it on my Mac, version 3.2.1 (2022-07-06), maybe it’s the issue of the Mac version?
oh my god (!) … no, no, it has nothing to do with the MAC … there is a principle bug inside: I cannot load any PDB file correctly with version 3.4 (I just compiled Blender)! The same applies with the patch of course … . I need to see what has happened … . 
So, for you, please, downgrade Blender and use 3.2.0. There, everything still works … .
To all of you, who work with Blender version > 3.2.0!
The PDB add-on does not work, it is broken! => The balls are not displayed.
I’m quite busy with other things atm and need to see when to deal with this HUGE bug … . So far, use Blender version 3.2.0, there, everything should be okay … .
I’m sorry for those circumstances … .
Blendphys.
EDIT: There seems to be a problem with the NURB balls, if one chooses Mesh balls, everything is fine! To be solved … we will see …
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3.2.0 does not work either, 2.93.10 works though. Let me try to put the latest patch. Thanks! @Blendphys
@Blendphys I tried 3.4 Alpha still not able to give me ball like representation.
wenchangyu2006, thanks for your kind help.
Please, can you try out if the newest Blender versions work when you choose Mesh spheres as balls?
Dear all.
The problem with the NURBS balls seems to be within Blender. The bug is described here on the Blender pages. Let’s see and wait … I keep you all informed.
Blendphys.
Dear all.
The problem with the NURBS balls has been fixed now, see here. What you need to do is to download the latest builds of Blender (starting with 3.5.0 alpha) or to compile the latest developer version or just to wait for the new release 3.5.0.
Cheers,
Blendphys.
Dear all,
I’m new to Blender and modeled a nanotube using it and when I tried to export the atomic coordinates of my model as .xyz and .pdb, I found that the coordinates were not saved. I wonder if we can’t get atomic coordinates in Blender? Could you please let me know how I can obtain it if it is possible? I would be glad if you help.
Cheers.
Derman
Hi drmnbastrkDerman.
Nanotube in form of atoms? It is not quite clear what you are trying to do. PLZ, can you send us the PDB or/and XYZ file such that we can follow your question? Thanks in advance.
Blendphys.
Hello,
Thank you for your interest. 
Since I am new to Blender, I followed a tutorial on YouTube. I guess I can’t send files because I’m a new user, so I’ll send them via WeTransfer. The model I made is as follows: https://we.tl/t-mABsApeJrI
.pdb file contains the following information:
REMARK This pdb file has been created with Blender and the addon Atomic Blender - PDB
REMARK For more details see the wiki pages of Blender.
REMARK
REMARK
Thanks.
Derman
Hi drmnbastrkDerman,
very nice! Have you done this or did you obtain this from some add-on? - The point is that another ‘Blender structure’ is used, which is not the same as the instancing-vertex-structure for the XYZ add-on (Link). So, this means that the XYZ add-on does not find the XYZ coordinates and exports basically an empty file … .
In your case, the coordinates are inside this ‘Vertex Groups’, right? Plz, can you send me the link of the tutorial? Thx.
Hi again,
Here’s what I did: I took the nanotube structure from the tutorial here and made the model helical using ‘curvature’. The coordinates might not be in the vertex group as you mentioned.
Thanks.