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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
3.12.5 (main, Aug 6 2024, 19:08:49) [Clang 15.0.0 (clang-1500.3.9.4)]
CP…
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From PIR-PRO discussion: It is possible that the mapping between types of modifications and the color used to display them is incomplete. @Julie-Cowart will find the source of the mapping in the code.…
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I could not run plmDCA with the latest docker environments. It kept crashing. I tried to resolve the issue, but I could not.
Following is the error message.
`[2019-11-12 15:06:28.109831] potts ru…
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It's useful for S-S bond to guide tleap.
What do you think?
```python
bonds = [(10, 20), (100, 200)] # List of atom pairs
parm.write_pdb(...., conect=bonds)
```
Note: not write all 'CONECT'…
hainm updated
2 years ago
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I tried to run a sequence design experiment with HES + 10-step lookahead on 10 sequences.
I initialized 2000 sequences for training reward model. With 2000 sequences, we can achieve Rsquared ~ 0.5 wi…
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## The need
The BLAST functionality of the interactive interface can only use nucleotide sequences. In the case of working with amino acid sequences in the interface provided by the `--fasta-file` …
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## 🐛 Bug
I am currently trying to analyze BCR sequencing data by using IMGT HiV-QUEST data before using immunarch for further analysis. I should note that I am analyzing BCR data from Rainbow Trout (…
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**Details**
I am trying to follow the protocol of Bae, J.W., Kwon, S.C., Na, Y., Kim, V.N., and Kim, J.-S. (2020). Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid …
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Hi,
I ran a DIANN search on samples that have been enriched for K-GG modification. I included C carbamidomethylation, Ox(M), and K-GG as modifications, and 2 max variable modifications.
While a…
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From https://github.com/pombase/pombase-chado/issues/52#issuecomment-2330349791
Here is a sample of the "Modified residue" data:
SPAC144.13c; │ MOD_RES 62; /note="Phosphoserine"; /evidence="E…