Dear all,
I am trying to access the Rosie webserver, but apparently it is not recognizing my institutional email.
Institution: Instituto Superior Técnico, Universidade de Lisboa
Domain: @ctn.tecnico.ulisboa.pt
I am trying to score how well different protein models fit into one electron desity map. I have tried using the score_jd2 tool with the flags:
"-database /programs/PDB/rosetta-3.13/main/database -in:file:s ./structures/*.pdb -edensity:mapfile ./emd_12705.map -edensity:mapreso 3.6 -edensity::realign min -cryoem_scatterers true -grid_spacing 2.0 -fastdens_wt 35.0"
Hi all,
I'm trying to use simple_cycpep_predict with crosslinker BBMB, and the generated structure (see attached) does crosslink with BBMB. However, it also does a head-to-tail cyclization between the 2 termini and I would like to not have that happen. It's not clear to me from the help file how to do that as the default uses head-to-tail cyclization. Is there a way to turn that off?
Here is the sequence file, the parameters that I'm using, as well as one of the generated structures to illustrate what I am having issues with.
Hi there,
One problem with the initial use of antibody application is that there is complie issue shown as the following:
Hi ROSIE and FARFAR2 team,
Hello all,
Using this command to graft from a specific template
antibody.mpi.linuxgccrelease -antibody:blastp /home/rosetta/ncbi-blast-2.13.0+/bin/blastp -fasta antibody.fasta -antibody:h1_template pdb_id
The modelled structure does not have constant portion of the antibody.
Hello
I am trying to model a modified 3D RNA structure using farfar2.
Job 「№108206」has failed with the message: No output silent files were produced in the FARFAR2 step; please double-check your inputs!
I have checked the input sequence and dot bracket files (PDB file exceeds the maximum allowed size for upload). I don't know, how to solve it. Attaching the input flies. Could someone please help me sort the error.
Thank you
I am following the rosetta tutorials and run into an error when attempting to relax a pdb for refinement. The "flag_input_relax" file cannot be opened by rosetta, even though I've granted myself full permissions and even changed it into an executable via chmod 755. I made a copy of the file and it could not open the copy either. Below is the command that gives me the error:
rosetta/main/source/bin/relax.default.macosclangrelease -in:file:s ~/rosetta/main/demos/tutorials/input_and_output/input_files/from_rcsb/1qys.pdb flag_input_relax
Hello all,
Using this command to graft from a specific template
antibody.mpi.linuxgccrelease -antibody:blastp /home/rosetta/ncbi-blast-2.13.0+/bin/blastp -fasta antibody.fasta -antibody:h1_template pdb_id
Can we use the same approach for grafting where we dont have a pdb id to specify template and use a specific structure instead ??
