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Not so much a bug as how best to communicate / prevent issues -- the naglrc3 model was not trained with single ions and does not accept single atoms with 0 bonds as an input feature (bond connectivity…
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Thank you for developing chai-lab, which is an amazing tool and has greatly assisted my work. However, when I try to input the trivalent iron ion in the ligand part locally using chai_lab with the com…
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One of the changes we made to the RDKit for the upcoming 2024.09.1 release (in [PR 7491](https://github.com/rdkit/rdkit/pull/7491)) was to remove the chemically unreasonable valence state of 7 for P a…
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@kkthek @CamAnNguyen
Different counter ions for the same charged molecule could be added as R-groups. For this, R-groups need to exist unconnected in the drawn structure and include the charged count…
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Hello everyone,
I am using DIA-NN to analyze ultralow sample data acquired with diaPASEF and VistaScan modes from timsTOF Ultra 2.
Multiple peptides of interest fall outside of the fragmentation win…
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Dear Developers,
I am encountering an issue while simulating DNA with implicit solvent using OpenMM. My system consists of two DNA strands and several Na ions. I have observed that the Na ions move…
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Several ions did not pass visual/logical value tests after the EC1 workshop. After manual investigation of the values, we are re-running samples in this file: [Data/ions/EC1_ions_rerun.csv ](https://g…
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```
msstore publish app.bbsync.BlackboardSync.msixupload --appId *** --noCommit -v
09:13:54 info: Microsoft.Hosting.Lifetime[0] Application started. Press Ctrl+C
to shut down.
09:13:54 info: Mi…
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output, incident, stopped = compound_bca_list_1D_py(
ux, uy, uz, energies_eV, [ion['Z']]*number_ions,
[ion['m']]*number_ions, [ion['Ec']]*number_ions, [ion['Es']]*number_ions, [targ…
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Check with @jorainer how I've listed background ions.