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If I build a DSSP file with the current mkdssp (which corrects along-standing bug in assigning secondary structure, by assigning polyPro helices "correctly" - see https://github.com/PDB-REDO/dssp) I g…
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Hi,
I have sucessfully runned colabfold_search locally using the following command:
```
colabfold_search \
--threads 32 --use-env 1 --use-templates 1 \
--mmseqs mmseqs \
--db1 /home/jflucier/p…
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In the recent fix to search for templates when a3m MSA is present:
https://github.com/sokrypton/ColabFold/blob/10b425d76c743eb3ece8b3dc68e117d0b2a89a16/colabfold/batch.py#L1336
isn't the get_msa_and…
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## Expected Behavior
Makes database with user supplied .a3m file(s)
## Current Behavior
Erorr of: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 36: invalid start byte
##…
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## Expected Behavior
Hi, BFD database is so huge that I am looking for a solution to compress it. Could you provide the compressed version of BFD database, that is, ca3m database? Or can you show me …
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After successfully installing RF2NA in my linux workstation, I tried to run these commands
```
# run Protein/RNA prediction
../run_RF2NA.sh rna_pred rna_binding_protein.fa R:RNA.fa
# run Protein…
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runs normal, however, there is no pdb file out in the result folder
$ run_pyrosetta_ver.sh XXX.fasta .
Running HHblits
Running PSIPRED
Running hhsearch
Predicting distance and orientations
Ru…
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Hello everyone,
I installed the ProSPr Docker container.
When I try to run ProSPr on a sequence using the command:
`docker run -t -v /home/dante/data/:/data prospr/prospr -t --a3mfile /home/dant…
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Anyone tried building their own databases for hhblits ?
I mean that from a protein fasta file to hhblits database.
I am using the pipeline listed in wiki of hhsuite:
https://github.com/soedinglab…
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Hi,
Your paper claims:
> "We use of the default AlphaFold-Multimer MSA search setting with JackHMMER to search the UniProt database for MSA pairing."
However, after examining the provided code …