Ieremie Ioan

icon location PhD student at University of Southampton. Vision, Learning & Control group.

Results 13 comments of Ieremie Ioan

Error in building with setup.py

You need to install the dependecies

I use command: pip install pymesh2,got an error

Any update on installing this on M1 macbooks?

I use command: pip install pymesh2,got an error

> Any update on installing this on M1 macbooks? After two days of banging my head, I managed to install it on my M1 MacBook Pro: Follow the instructions from:...

building for macOS-x86_64 but attempting to link with file built for macOS-arm64 Undefined symbols for architecture x86_64:

After two days of banging my head, I managed to install it on my M1 MacBook Pro: Follow the instructions from: https://pymesh.readthedocs.io/en/latest/installation.html 1. Install the third party dependencies using Macports,...

[Question] How do I cluster Uniref90 after it has been translated into a 5 letter alphabet?

Hi @milot-mirdita, thanks for the quick reply! I am not creating a new substitution matrix. I am using the default parameters. Increasing the k-mer size seems intuitive, I'll try that....

[Question] How do I cluster Uniref90 after it has been translated into a 5 letter alphabet?

Hi @milot-mirdita. I've done a parameter search over the kmer length and number of kmers. It seems that for small alphabets there is a need for a higher number of...

[Question] How do I cluster Uniref90 after it has been translated into a 5 letter alphabet?

Thanks for the response @milot-mirdita. I've explored that parameter too. It seems that Kmer length: 25 | Nr kmers: 160 works the best for small alphabets. I'll see if using...

ShrakeRupley fails on structures containing deuterium (D) atoms

Probably the best fix is using the atom RADII values used in calculating the atom's distance to surface. The dictionary there covers all the possible atom types (as used in...

ShrakeRupley fails on structures containing deuterium (D) atoms

Hi @tomerco4, that would fix the problem, but it would give a RADII value of 2 to all unknown atom types. However there is a complete radii dict used in...

MMseqs2 hangs at prefilter stage with large database (1B sequences, 4.1TB) using MPI + GPU build

> We no longer actively develop MPI, while still testing it. Also we did not implement MPI support for GPU usage. It is likely more effective to manually split the...