lh12565

> > Did you mean add device: cpu to the config/generate.config? like this: > > Yes. > > > It still reported the same error. > > Did you `git...

Hi @mattragoza I guess I can use dock model, such as autodock, to determine ligand coordinates and the grids. right? Thanks!

Hi @mattragoza I still have some issues to solve it. （1）I try to run the two models (using prior: 0): protein with a known ligand and pocket, protein with the...

> I recommend [meeko](https://github.com/forlilab/Meeko) instead of `prepare_ligand4.py`. The input needs to be 3D and protonated, and SD files are preferred to MOL2. > > The PDBQT files do not define...

> You may have to call mol.assignHelixSheet on the structure, as soon as you load it. It might also be that that structure has no secondary structure? What is the...

> Hello, P48980 looks to be a much larger structure than appears in your image? Do you call assignHelixSheet after you load the structure? > […](#) > On Thu, 1...

> pv.io.fetchPdb('alphafold.pdb', function (structure) { **mol.assignHelixSheet(structure);** viewer.cartoon('structure', structure); viewer.autoZoom(); viewer.fitParent(); }); Thanks! It works.

> By default, each run of `biobloommaker` produces one filter (`.bf`) per command. That is using a single fasta file should collapse it into a single filter. For example: >...

> Try something like > > ``` > biobloommaker -p hb hb.kc.fa > biobloommaker -p hbv hbv.kc.fa > biobloommaker -t 10 -p human Homo_sapiens_assembly38.fasta > > biobloomcategorizer -t 40 --fa...

Hi, @JustinChu I found if I used the k-mer fasta to run biobloomcategorizer, there is no hit in this fasta. But if I used the raw fasta, I got some...