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I work at the APHP, a university hospital linked to the university of Paris, and in a research unit of INSERM, the French national institute of health and medical research. The email addresses of these 2 organizations are not listed: aphp.fr and inserm.fr. Is it possible to add them ?
Hello Rosetta users,
I have a few questions with respect to antibody modelling in Rosetta.
The current version of Rosetta I'm using is a pre-compiled version 3.13 of Linux. I always get an error when I perform the first step of Antibody Modeling:
antibody.static.linuxgccrelease \ -fasta antibody_chains.fasta
I checked and found that the solution to this problem was to install a higher version of GCC.
I'm trying to use simple_cycpep_predict with the option thioether_lariat for cyclization_type but seem to be running into a problem. Based on what I read in the help docs, "thioether_lariat" should be an option that is possible, but when I tried to use it, I get:
ERROR: Illegal value specified for option -cyclic_peptide:cyclization_type : thioether_lariat
Is this an option that got removed and the help pages just weren't updated? Or am I missing something? I am attaching the the sequence that I am trying to model.
I am using min_mover (lbfgs_armijo_nonmonotone) for minimizing the energy function of a protein for structure prediction in pyrosetta.
In trying to get an energy plot over iterations, i set min_mover.max_iter(1) to 1. After each iteration of min_mover, I pause the optimization, store the current energy, and continue.
I want to use RoseTTAfold on the Robetta.new server but it requires an a3m file I dont know how to generate.
I saw a script on the github page (https://github.com/RosettaCommons/RoseTTAFold/blob/main/input_prep/make_msa.sh) that to my understanding is supposed to convert fasta to a3m but it dosent seem to work and I get the following error: