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Hello all,
thank you for the update! However now we are running into a new error while testing on a bunch of different GPUs. This is on our HPC.
```
#!/bin/bash
#SBATCH --nodes=1
#SBAT…
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My trajectory contains ASH residues, which is protonated ASP for AMBER, albeit non-standard.
I guess `Toplogy.select('protein')` fails to parse atoms in such residues as protein, since `__AMINO_ACI…
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```
What steps will reproduce the problem?
1. Read 2ezs for NRG-CING.
complete list potentially affected:
1crq 1crr 1ezc 1ezd 1kld 1l0r 1qch 1r4e 1sah 1saj 1vve 2axx 2ezq 2ezr 2ezs
What is the expec…
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Hi, is it possible within NGL?
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Hi @wojdyr and everyone,
Should [OBSLTE](https://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#OBSLTE) be added to Structure::info as the cif tag _pdbx_database_PDB_obs_spr or…
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I need to be able to parse .cif files so that I have access to the complete protein chain sequence along with annotations for which residues are unobserved or 0 occupancy.
For example, for a protei…
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Speaking personally, the best outcome of this would be to find that someone has already solved the problems we're thinking about, or at least at least has a solution that can be extended to cover this…
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I am not sure where I can find the updated file.
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Just of the top of my head...
PDB
* Validation reports
* Electron Density Maps
* Others (listed in the PDBe API 'files' endpoint, e.g. http://www.ebi.ac.uk/pdbe/api/pdb/entry/files/1cbs)
Uni…
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See https://github.com/ihmwg/IHMCIF/pull/104 for details
- [x] Add `_struct.pdbx_structure_determination_methodology` and the corresponding vocab table
- [x] Add `ihm_ordered_model`
- [x] Add …