Hongbin Liu

More Explanation for the CGC-finder output?

1

Hi! Thank you for the great tool! I just used and cited this tool in my paper! Now I'm confused about the output of CGC-finder.  1. what are the...

Hi, I'm trying to install the UDSMProt through `conda env create -f proteomics.yml`, but incompatible packages were found. Could you provide an updated proteomics.yml file? Thanks!

libatomic.so.1 not found

1

## Expected Behavior Compile the specific version [MMseqs2 71dd32ec43e3ac4dabf111bbc4b124f1c66a85f1 (May 28, 2023)](https://github.com/soedinglab/MMseqs2/archive/71dd32ec43e3ac4dabf111bbc4b124f1c66a85f1.zip) under Linux I encounter a similar error as [here](https://github.com/soedinglab/MMseqs2/issues/480). And the mentioned package `libgcc-ng` has been installed. ##...

:exclamation: Make to check out our [User Guide](https://github.com/soedinglab/hh-suite/wiki). ## Expected Behavior `hhblits -cpu 20 -i A0A0K3ARH1.fa -d /work/home/ac1daawz21/software/DPAM-main/DPAM/UniRef30_2022_02/UniRef30_2022_02 -oa3m A0A0K3ARH1.a3m` ## Current Behavior I tried to run the code above,...

database download manually

10

## Expected Behavior Could the pre-processed PDB and Alphafold/Swiss-Prot database be downloaded manually? ## Current Behavior Could not download the database with script `foldseek databases PDB pdb tmp`. And the...

Cluster purity analysis with structurealign?

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## Expected Behavior Hi, I found the cluster purity analysis using structurealign here (https://www.biorxiv.org/content/10.1101/2023.03.09.531927v1). The representative structure was aligned to the cluster members using the "structurealign -e INF -a" module...

a PDB list as input for foldseek?

2

HI, for the `easy-search` , `foldseek easy-search example/d1asha_ example/ aln tmpFolder` , could the `example/` be replaced by a txt file that contain a list of structures (might from different...

understanding the similarities of hits?

2

## Expected Behavior Hi, I'd like to make sure that my understanding of the `foldseek easy-search` hits is correct. By default ( `--alignment-type 2` ,without TM-align), the TMscore used for...

docker image for cuda11.1?

41

Hi, I found that the [available docker images](https://github.com/sokrypton/ColabFold/wiki/Running-ColabFold-in-Docker) are compatible with the CUDA 11.8 and 12.2, respectively Would you please build a docker image for cuda 11.1 or 11.2? Many...

Hi, I installed the MPA in Linux with Conda. I encountered the following error. Could you help me with this error? Thanks! (MPA) liuhongbin@slurm-master:~/database/PAT/toxin/metaproteomics$ mpa-portable de.mpa.cli.CmdLineInterface -spectrum_files BGA04F14.mgf -database test.fasta...