I get the error below when trying to import a pdb-file, online or localy.

I have followed the steps in the instalation guide: I run Blender as an administrator on Windows 10, and after installing the add-on, i click the button to install Atomium. I get a confirmation that Atomium is successfully installed.

In the MolecularNodes panel i click the "Download" / "Open" button and get the error below. I assume the it is because the Atomium library is not properly installed.

Python: Traceback (most recent call last):
  File "C:\Users\Jonas\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 1401, in execute
    sna_func_import_structure_EE5B6(bpy.context.scene.sna_pdb_code,
  File "C:\Users\Jonas\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 1134, in sna_func_import_structure_EE5B6
    pdb = atomium.fetch(pdb_id)
UnboundLocalError: local variable 'atomium' referenced before assignment

location: <unknown location>:-1

I am very curious to try this amazing add-on, hope that you can help resolve the issue.

Hi!

I installed MolecularNodes, both the add-on and the atomium installation was said to be fine. However, when I tried to load a pdb file (even from pdb or file), I get the following error: Blender version: 2.93.4, add-on version: 0.4.0

What could the the issue?

Hi, I'm trying "Download from the PDB" and "Load MD Trajectory File" according to your document. However, I got the same error in both cases. Thanks!

Python: Traceback (most recent call last):
  File "C:\Users\ryohei.yamaguchi\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 2471, in invoke
    return self.execute(context)
  File "C:\Users\ryohei.yamaguchi\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 2458, in execute
    sna_func_import_structure_EE5B6(
  File "C:\Users\ryohei.yamaguchi\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 1583, in sna_func_import_structure_EE5B6
    sna_setup_node_tree_272D6(output_name, unique_chains, base_model,
  File "C:\Users\ryohei.yamaguchi\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 2599, in sna_setup_node_tree_272D6
    create_starting_node_tree(collection_of_properties=col_properties,
  File "C:\Users\ryohei.yamaguchi\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 2523, in create_starting_node_tree
    node_input = node_mod.node_group.nodes['Group Input']
KeyError: 'bpy_prop_collection[key]: key "Group Input" not found'

location: <unknown location>:-1

Excited to see this! Blender wouldn't let me enable the plugin saying it crashed on line 23 of __init__.py file (see source below). I was able to just install atomium by copy/paste the install script in repo though. This was on Blender 3.0.0

bl_info = {
    "name" : "Molecular Nodes",
    "author" : "Brady Johnston", 
    "description" : "A plugin and nodes for working with molecular data in Blender.",
    "blender" : (3, 0, 0),
    "version" : (0, 3, 2),
    "location" : "Perth, Australia",
    "waring" : "",
    "doc_url": "", 
    "tracker_url": "https://github.com/BradyAJohnston/MolecularNodes/issues", 
    "category" : "Molecular" 
}

import bpy
import bpy.utils.previews

import subprocess
import os
import bpy
import bpy
import os
import bpy
import atomium # error here

I have a little hydrogen peroxide pdb file that looks like this:

ATOM      1  O   PER     0       0.038  -0.113  -0.046  0.00  0.00           O  
ATOM      2  H   PER     0       0.132  -0.803  -0.752  0.00  0.00           H  
ATOM      3  O   PER     0      -1.074  -0.427   0.586  0.00  0.00           O  
ATOM      4  H   PER     0      -0.777  -0.749   1.475  0.00  0.00           H  
END

When I load it with MolecularNodes it seems to become three oxygens and one hydrogen. I notice that the auxllary object ohoh_properties_1 only has three vertices, where I would have expected four. The x-values of the vertices are 8.0, 1.0, and 8.0, which I assume are the atomic numbers. Nothing seems to tell Blender that the last atom is a hydrogen. I spotted a potential too short range in create_properties_model, in which case one should remove '-1' from the following: locations=list(map(lambda x: [get_value(prop_x, x), get_value(prop_y, x), get_value(prop_z, x)], range(len(first_model.atoms()) - 1))))

Hi all, I am getting the following error, when trying to add the Ribbon style node, under Styling-Style ribbon. (The same thing happens when trying to add any of the nodes from the Molecular Nodes package). Thanks!

Python: Traceback (most recent call last): File "C:\Users\sarah\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes_init_.py", line 2501, in invoke return self.execute(context) File "C:\Users\sarah\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes_init_.py", line 2495, in execute bpy.context.active_node.node_tree = bpy.data.node_groups[ AttributeError: 'FunctionNodeRandomValue' object has no attribute 'node_tree'

location: :-1

Hey :)

It seems that "not alpha carbon" doesn't select non-alpha carbon on my example (here I remove all non-alpha carbon):

https://user-images.githubusercontent.com/8037224/169951938-d6b82adb-70d3-4475-a377-317a18b490fa.mp4

Hi Brady :-)

Thank again for this wonderfull addon =D I was trying to set it up on my MacBook Pro, and It didn't work because blender didn't find atomium (despite the installation ended up well). After some investigation I saw that all tools were install in my Home directory ~/.local/lib/python3.10/site-packages instead of the blender directory (/Applications/Blender.app/Contents/Resources/3.1/python/lib/python3.10/site-packages)

Quick and dirty fix : mv ~/.local/lib/python3.10/site-packages/* Applications/Blender.app/Contents/Resources/3.1/python/lib/python3.10/site-packages/

Now it works, but I just wanted to reported it if anyone have the same issue at some point :-)

I was trying to debug why my generated PDB files were not working and I think I tracked it down to the import_protein_local function.

If I try enter PDB code and download, all is good.

But if I manually download, enter the location of pdb file, I get this error:

The frames are not imported.

Here is the pdb file I tried: https://files.rcsb.org/view/7QIL.pdb

And last one of today's batch 😅

when I tried to insert a node "selection > AA Name", nothing happens and no new nodes are inserted...

Cheers! Thibault.

Hi again :)

I wanted to try the "test_chain_selection" node but it return a python error when an MD is loaded (I haven't tried yet with a static PDB)

Python: Traceback (most recent call last):
  File "C:\Users\tubia\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 604, in invoke
    return self.execute(context)
  File "C:\Users\tubia\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 417, in execute
    bpy.ops.wm.append(
  File "C:\Program Files\Blender Foundation\Blender 3.1\3.1\scripts\modules\bpy\ops.py", line 132, in __call__
    ret = _op_call(self.idname_py(), None, kw)
RuntimeError: Error: 'C:\Users\BradyJohnston\Documents\GitHub\MolecularNodes\molecular_nodes_append_file.blend\NodeTree\MOL_utils_bool_chain': not a library


location: <unknown location>:-1

Cheers! Thibault.

I keep getting "Error: MDAnalysis Unavaiable" despite having MDanalysis installed. I just followed the instructions, and installed:

• Blender 3.1.2 (ok)
• Molecular Nodes 0.5.19 (ok),
• Atomium (ok),
• python3 -m pip install MDAnalysis (ok)

However, I keep getting the error "MDAnalysis Unavaiable" (I obtain the path from import MDAnalysis as mda; mda.__path__)

I'm trying to load a PDB from a MD simulation from a folder. It has no 4-character code and all the times i tried to, it failed.

Is there a way to load a "custom" pdb or only from PDBDatabank?

Thank you!

Currently there is no way to select, delete or distinguish water molecules in the structures that are imported.

Having a is_water property would fix this issue.

Hi Brady,

I have a local PDB file, attached as CTD.zip. It is self-generated so that it has nothing else but only the atom position information. It can be opened in PyMol or ChimeraX. But when I load it via Molecular Nodes, it tells the following error.

Python: Traceback (most recent call last):
  File "C:\Users\luod\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 1491, in execute
    sna_func_import_structure_EE5B6(
  File "C:\Users\luod\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 907, in sna_func_import_structure_EE5B6
    n_atoms = len(first_model.atoms())
AttributeError: 'File' object has no attribute 'atoms'

location: <unknown location>:-1

My ultimate goal is to convert this CTD.pdb into mmCIF (with more than one instance of the protein in mmCIF, and hence with transformation info) and then combine multiple proteins' mmCIFs into one big mmCIF. The final mmCIF will have more than 99,999 atoms for sure. So I can only rely on mmCIF format. I tried several tools (mmcif.pdbj.org converter, export from PyMol/ChimeraX, gemmi, pdb-tools). None of them give me a successful loading. The mmcif.pdbj.org converter does seem promising in my case, as the converted file (CTD.pdb.zip) gives the same error as above. And I also noticed that if I convert in this way for 1bna, the converted mmCIF can indeed be loaded via Molecular Nodes. However, I do want to rely on a command-line tool to finish the format conversion as I have a handful of PDBs to be converted.

My guess is there is some metadata that is required to be in the PDB/mmCIF either from the Molecular Nodes side or from the Atomium side. But this info might not actually be that necessary.

Anyways, it would be great and be appreciated if you can help with the debugging. But I would also like to set up a debugging/dev environment. This is the first time I use both Blender and its python addons. But I have some experience using PyCharm/VS/VS code. Could you please guide me shortly on how to set up the dev env? Thanks.

Runninng list of compatibility issues with the new Blender 3.2 beta release and upgrades of nodes and interface required for a 1.0 release with Blender 3.2.

Will be targeting a 1.0 release of Molecular Nodes to coincide with Blender 3.2 release, which will bring named attributes to GN and make the Molecular Nodes nodes much cleaner and easier to work with.

Import

• [x] Create panel for MD trajectory import

• [ ] Improve Bond Calculations on Import

  • [x] LImit to within chains
    • [x] Exceptions for disulphide bonds
  • [ ] Confirm radii for usage in algorithm
  • [ ] Attempt to speed up with numpy

• [x] upgrade Find Bonds node to take into account chains

• [x] Add automatic setup of animat frames nodes for multi-state PDB files

MDAnalysis Compatability

• [x] Confirm import of all properties
• [ ] Add per-frame b-factor import
• [x] Enable detection of MDAnalaysis by Blender python installation
  • [x] Improve detection of MDAnalysis once installed
• [x] Enable automatic setuyp of animate frames nodes for MD trajectory files
• [x] re-order properties to align between MDA and atomium import strategies

Interface

• [x] Addition of geometry node modifier doesn't auto-create and assign a new node tree, so setup of default nodes fails.
• [x] Add tooltips to all interface items.

Nodes

• [x] Upgrade Find Bonds node to take into account atomic radius element
• [x] Upgrade colour node to use attributes
• [x] Upgrade selection nodes to use attributes
• [x] Upgrade EEVEE atoms node to utilise instancing and materials attributes
• [x] Add invert button for object effect
• [x] Fix the animate_frames node to not be relative to original position, breaks when atoms teleport to the other side of the simulation box
• [ ] Add per-chain custom colour node
• [ ] Update custom chain selection node to use named attributes

Documentation

• [x] Documentation for Atomium Install
• [x] Documentation for MDAnalsysi install and linking
• [x] Documetation for PDB Download
• [x] Documentation for opening local file
• [x] Documentation for MD Trajectory import
• [ ] Nodes Documentation
  • [ ] Atomic Properties Documentation
  • [ ] Animate Frames Documentation
  • [ ] Styling nodes documentation

Hello Brady :)

Long time ago I made a video on VMD of my Norovirus Capsid, and I thought that it could be a good test for your tool (Since I have 600K+ atom in the PDB). Here it is (just 1 state) morph_state001-capsid.zip

The problem is that only one part seems to be read since the numbering stop at 99999 (cf. Screenshot 1). I tried different format (convertion with Pymol to mmtf, mmcif, cif, pdb.gz, cif.gz) and it fails for other format (But here the problem seems to come from the atomium library for reading mmtf or mmcif when the output comme from Pymol maybe ?)

For this issue maybe the problem come from the atomium library itself ? But I wanted to repport it since with this new render system it seems possible to load very big systems, and unfortunatly the "assembly" coming from the PDB is splitted into different models (so your addon think it's a trajectory)

Anyway, here's some extra information ⤵️ and thank you again for this already great piece of work =D Thibault.

Screenshot 1:

traceback for loading when it's mmtf

Python: Traceback (most recent call last):
  File "C:\Users\tubia\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 80, in execute
    sna_func_import_structure_EE5B6(bpy.context.scene.sna_pdb_code,
  File "C:\Users\tubia\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 1137, in sna_func_import_structure_EE5B6
    pdb = atomium.open(pdb_path)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\utilities.py", line 41, in open
    return parse_string(filestring, path, *args, **kwargs)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\utilities.py", line 122, in parse_string
    parsed = file_func(filestring)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\mmtf.py", line 18, in mmtf_bytes_to_mmtf_dict
    return decode_dict(raw)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\mmtf.py", line 40, in decode_dict
    new_value = [decode_dict(x) for x in new_value]
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\mmtf.py", line 40, in <listcomp>
    new_value = [decode_dict(x) for x in new_value]
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\mmtf.py", line 37, in decode_dict
    new_value = parse_binary_field(new_value)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\mmtf.py", line 56, in parse_binary_field
    codec, length, params = struct.unpack(">iii", b[:12])
struct.error: unpack requires a buffer of 12 bytes

location: <unknown location>:-1

Traceback for loading when it's mmcif

Python: Traceback (most recent call last):
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\pdb.py", line 506, in add_atom_to_non_polymer
    ] = atom_line_to_dict(line, aniso_dict)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\pdb.py", line 530, in atom_line_to_dict
    a["x"] = float(line[30:38].strip())
ValueError: could not convert string to float: '9 ? -57.'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\tubia\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 80, in execute
    sna_func_import_structure_EE5B6(bpy.context.scene.sna_pdb_code,
  File "C:\Users\tubia\AppData\Roaming\Blender Foundation\Blender\3.1\scripts\addons\molecular_nodes\__init__.py", line 1137, in sna_func_import_structure_EE5B6
    pdb = atomium.open(pdb_path)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\utilities.py", line 41, in open
    return parse_string(filestring, path, *args, **kwargs)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\utilities.py", line 124, in parse_string
    parsed = data_func(parsed)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\pdb.py", line 86, in pdb_dict_to_data_dict
    update_models_list(pdb_dict, data_dict)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\pdb.py", line 158, in update_models_list
    add_atom_to_non_polymer(line, model, res_id, aniso, full_names)
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\pdb.py", line 512, in add_atom_to_non_polymer
    "atoms": {int(line[6:11]): atom_line_to_dict(line, aniso_dict)}
  File "C:\Users\tubia\AppData\Roaming\Python\Python310\site-packages\atomium\pdb.py", line 530, in atom_line_to_dict
    a["x"] = float(line[30:38].strip())
ValueError: could not convert string to float: '9 ? -57.'

location: <unknown location>:-1