Raul Araya-Secchi issues

Results 5 issues of


                                            Raul Araya-Secchi

Using recent pdbs (or a more recent version of pdb70) to search for templates.

Hi, I will like to consider in the search for templates very recent structures available on the PDB. However, when I try to use the colabfold_batch (https://github.com/YoshitakaMo/localcolabfold) I only get...

Unable to cluster large set of similar proteins

I'm trying to cluster a set of ~500 conformations of the same protein but no matter what I try I only get 1 cluster. Do I need to do something...

Question: How can I use the same set os sequences or same alignment for a batch of input sequences to model

I'm generating models for a batch of closely related sequences and I will like that the alignment used for the generation of the models contains the same sequences for each...

Jax issue after update

Hi, I just updated and got the following error on execution: 2025-01-20 12:28:47,565 Running colabfold 1.5.5 (406d4c6cf25a0755f61b3adac7c5d47d3025f42c) 2025-01-20 12:28:47,577 WARNING: no GPU detected, will be using CPU Traceback (most recent...

Is there a sequence similarity threshold to get AF2 to use the custom template?

Hi, I'm trying to use custom templates to generate model for a protein using AF2-multimer V3 with the following command: ~/bin/localcolabfold/colabfold-conda/bin/colabfold_batch --num-recycle 5 --num-ensemble 5 --model-type alphafold2_multimer_v3 --num-models 5 --amber...