T008-T010: Cannot download PDB structure via MMTF API anymore

[Q84-wq]

Hello,
I want to notice that the support of mmtf.rcsb.org is no longer available, so the function mmtf.fetch() in opencadd.Structure doesn't work anymore. I ask you, please, change this code so it can work. If you know the avaliable url for mmtf library, I could change it in utils/constants, so I can use these talktorials.
It returns me Errno 11001: gaierror and URLError
Terminal: pip install mmtf-python
Console:
import mmtf
mmtf.fetch('4TRO')

4TRO is for example

[dominiquesydow]

Hello,

Many thanks for reporting this to us. Apparently the MMTF format is no longer supported by the RCSB and replaced by the BCIF format.
https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c

Hence, also the mmtf package, which is a Python implementation of the MMTF API, is not in use any more.

We will have a look how to use the BCIF API instead.

As the corresponding function in opencadd‘s Structure object mimics mdanalysis‘ Universe object, I think we also have to check in there.
https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/coordinates/MMTF.py#L56

@AndreaVolkamer is there anyone in your lab who can take a look at this or even has already dealt with this?

Many thanks!

[Q84-wq]

I also noticed that I couldn't install package teachopencadd where was function seed_everything () because of the tensorflow-base.2.18.0 (something like this). Conda told me that I had corrupted file, pip told me that there was parse-function problem(if I remember correctly). I only want to say that I could resolve this problem with the help of pip install pytorch-lightning=1.7.7, where pytorch-lightning utilities.seed had the same function.

[Q84-wq]

I am sorry for interrupting, I also have a question, when can the problem with mmtf package be resolved (changing the library, I mean)?
Anyway, thank you very much for noticing my message_s!

[dominiquesydow]

I also noticed that I couldn't install package teachopencadd where was function seed_everything () because of the tensorflow-base.2.18.0 (something like this). Conda told me that I had corrupted file, pip told me that there was parse-function problem(if I remember correctly). I only want to say that I could resolve this problem with the help of pip install pytorch-lightning=1.7.7, where pytorch-lightning utilities.seed had the same function.

Hi @Q84-wq, I moved this issue to a stand-alone issue: #421.

[dominiquesydow]

I am sorry for interrupting, I also have a question, when can the problem with mmtf package be resolved (changing the library, I mean)? Anyway, thank you very much for noticing my message_s!

Hi @Q84-wq,

I cannot give a good timeline as it is holiday season for most people in the lab atm and I am on mat leave. I'd think a couple of weeks at least to get all the updates in. I am very sorry for the inconvenience!

[dominiquesydow]

Progress on solving this issue on opencadd's end here: volkamerlab/opencadd#159

[itWangCode]

Sorry to bother you:
How to deal with Structure.from _ atomgroup ( complex _.select _ atoms ( f 'resname { ligand } ' ) )

---

ValueError Traceback (most recent call last)
Cell In[58], line 1
----> 1 ligands = [
2 Structure.from_atomgroup(complex_.select_atoms(f"resname {ligand}"))
3 for complex_, ligand in zip(complexes, pairs.values())
4 ]
5 ligands

Cell In[58], line 2, in (.0)
1 ligands = [
----> 2 Structure.from_atomgroup(complex_.select_atoms(f"resname {ligand}"))
3 for complex_, ligand in zip(complexes, pairs.values())
4 ]
5 ligands

Cell In[41], line 73, in Structure.from_atomgroup(cls, *args)
71 for a in args:
72 if len(a) == 0:
---> 73 raise ValueError("cannot merge empty AtomGroup")
75 # Create a new topology using the intersection of topology attributes
76 blank_topology_attrs = set(dir(Topology(attrs=[])))

ValueError: cannot merge empty AtomGroup