Comments (5)
Hi @ungsik, which version of moleculekit are you using? I believe I fixed all issues with these atoms in the last version.
To check the version run conda list moleculekit
in your conda environment
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Hm yes indeed. Ok I will have to take a look at it tomorrow. I will try to run the whole scPDB this time. I was having some issues with disk space last week and could not test it thoroughly. Sorry for this.
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Okay, with the last commit in github the issue you mentioned is fixed.
The molecules you mentioned above have multiple cofactors bound to the protein which need to be removed.
But there is also another issue with some terminal residues not recognized correctly as part of the protein due to missing bonds and bad topology. I will open a new issue on that. For now you could remove the terminal residues which are not recognized as protein if they are not close to the binding site but it might be a bad idea.
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Related Issues (20)
- Add support for preparing non-canonical residues with backbone modifications HOT 1
- Small molecule CIFs can have ? coordinates HOT 1
- Wrapping bug puts water atoms way outside the box in a small set of frames HOT 1
- Finding difference between voxels of two different protein HOT 1
- PIP incompatibility: filename has '1.2.0', but metadata has '0' HOT 5
- Protein atoms regarded as nonprotein atoms by atomselect() HOT 2
- Add sasa option to the atom selection language HOT 2
- Update getFingerprint in moleculekit HOT 2
- SmallMolLib unexpected behaviour HOT 4
- atomselect fails on resnames that start with number HOT 3
- Syntax error with atomselect HOT 6
- ImportError HOT 3
- Conda package contains `.h` and `.cpp` HOT 7
- `atomselect` doesn't recognize `numbonds` HOT 1
- Failed to parse selection resid<200 HOT 3
- ValueError: Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM HOT 6
- Editing velocity files HOT 2
- numpy version, infinite loop when calling Molecule HOT 2
- `atomselect` improvements
- Fix issue with terminal histidine protonation HOT 2
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