Rolando Rodriguez

Oh this is a good idea for sure ! In the meantime @BinhongLiu what I usually do for that is to symlink all desired PDB files to a single input...

@twaksman001 The ESM2 models are not integrated in the MGnify database or easily searchable in the EBI site, like it is the case of AlphaFold2 that is integrated with the...

Thanks for your swift reply Martin! Anything I can do to help having it implemented, just let me know ..

I just concatenated all the databases, but still will be good to be able to search on more than one.

Hi @milot-mirdita Probably the question also implies how to do, or where to place the NCBI tax db ? If I pass any of these parameters to` convertalis`, I get...

Right Milot (@milot-mirdita) .. is the databaseX_taxonomy But I see now that is not working on my full concatenated database .. and keep asking for the taxonomy files, because It...

Hi @marcus-r-kelly, @peterjc Still there is a problem and we don't have all the Enzymes from REBASE in BioPython, I just talked with the REBASE people and they were just...

Hi @peterjc I added a PR with the changes we made to the /Script/Restriction/ranacompiler.py to be able to import all enzymes from any EMBOSS files supplied or self generated .....

Hi @peterjc, I feel you .. here we can see some numbers: |DB|Enzymes|Suppliers|Types|Lines of Code| |----|:----:|:----:|:----:|:----:| |Emboss|1088|15| 51|24296| |Embossa|4874|15|56|107612| |Created by EMBOSS from withrefm|6062 total, 5713 parsed|15|41|125997| |Bairoch|14574 total, 4370...

You are right, we change the output format to make it more consistent on the number of blank lines .. but it was just output .. On the tests, @peterjc,...