Julia Varga

Custom-height letters

1

Hi! This is a great package and I would definitely use it a lot. I have a question: is there any way to provide custom-height metric to sequence logos? Like...

Generate alignments/give rotation&translation matrix

12

Hi, It is a very nice software and extremely fast, thank you! One question: would it be possible that the server provides the superimposed structures and/or the translation-rotation matrix for...

Protein secondary structure & domain annotation

6

Hi, this seems an awesome and very much needed package! I have 2 feature request: would it be possible to add protein secondary structure annotation (helices and beta-sheets) and also...

Feature request: sequence from uniprot id and residue numbers

2

Hi, These notebooks are super cool, thanks so much for the continuous updates. I have one feature request: pulling in sequences from UniProt ID-s, preferably also cutting needed residues. This...

Crashing of complex with 600 residues

2

We are running the following protein sequence with AlphaFold2-ptm, using the AlphaFold2_mmseqs2 notebook. It is approximately 629 AA long. I have a Colab Pro account, so RAM should not be...

Normal notebook crashing on multimer run

2

Hi, I was running a complex with the AlphaFold2.ipynb notebook (I only provided a sequence with : and a job name). This was the error I got when running the...

Running sleuth in single run mode

1

Hi! I have run kallisto on RNA-Seq data from SRA. Unfortunately, it does not have any replicates. After kallisto, I try to run sleuth with recommended commands (https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html). However, sleuth_fit...

Where to issue SSH tunnel command?

3

Hi, this seems like a lovely package, but I cannot get it to work. I am trying to connect to a server on a university system which is behind VPN....

Hi, I was running a PDB file with foldseek on the swissprot Af models, using TM-align option. I noticed something weird with the listing of the TM-score  (all results:...

Hi, I was doing the installation and was wondering if instead of downloading every databasem installing mmseqs2, etc. could a script be provided to query the mmses2 server as with...