-
Hi AF2 team!
I'm chiming in to see if you all might be open to modifying some of the Python wrappers to external tools such that they automatically use all CPUs available?
I did a quick audit of…
-
I saw the ECO sample file in the feature folder, each residue has only one feature, but I have 30 columns of features in the HMM file output using HHblits, how to calculate the ECO value? Is it possib…
-
## Expected Behavior
running a hhblits search should complete when searching with a sequence on a custom database
## Current Behavior
hhblits returns a segmentation fault
## Steps to Reproduce…
-
*** buffer overflow detected ***: psipred terminated
xx/1.0.0.2/RoseTTAFold/input_prep/make_ss.sh: line 19: 1324074 Aborted (core dumped) psipred $ID.mtx $DATADIR/weights.dat $DATADIR…
-
the script should live in: `scripts/calculate_Neff.py`
Once HHblits is completed we need to calculate the effective family size from `a3m` file.
N_eff = N_clu(%) / sqrt(N_aa)
depending on N_eff…
-
Hi, I'm trying to run model using an example file, but there's an error.
`$ ../run_RF2.sh rcsb_pdb_8HBN.fasta -o 7UGF`
```
Running HHblits
-> Running command: /home/yt/RoseTTAFold2/input_prep/m…
-
Hi! After running openfold according to the default configuration, I found that there was a big difference between the output pdb file of openfold and alphafold (colab version). After comparing the re…
-
Hello, thanks for the awesome contribution. @amorehead
when I run predication of some monomer in conda environment, it is terminated without any note. it occurs in Running HHblits stage and nothing i…
-
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…
-
Hi,
I installed RoseTTAFold-All-Atom exactly as instructed, and then completed missing packages,
2005 pip install hydra-core --upgrade
2007 pip install icecream
2009 pip install assertp…