The problem hasn't been solved
Friends,
In the latest rosetta, what this the correct executable to predict the 3D structure of RNA. I dnt find the rna_denovo.linuxgccrelease or rna_design.linuxgccrelease which was in version 3.1
Thanks,
Bala
Hi All!
I would like to load a protein structure together with a ligand. Subsequently, I want to get the interaction energy values (e.g., fa_atr, fa_rep,...) between all protein residues and each ligand atom or a subset of ligand atoms. Herewith, I want to decompose the ligand to analyze certain amino acid - ligand atom interactions.
How is it possible to calculate an emap that contains vectors for residue x ligand atom pairs?
Thank you very much for your help and any suggestions!
This works:
scorefxn = create_score_function('standard')
emap = core.scoring.EMapVector()
Hi all,
I am trying to figure out how to add coordinate constraints while doing loop minimization without success so far. I would like to constrain my loop CA atoms to their initial positions but if I add coordinate_constraint to my score function this has no effect as I suspect that I need to add constraints to my Pose object but I am not sure how.
Is this possible to do with PyRosetta?
thanks!
If possible, how do I do it.? Because I don't see any page in the manual that talks abt alanine scanning. Thanks.
Hi, I recently prepacked my protein-peptide complex for use of flexpepdock and I realised that the OXT atoms existed at individual oxygen atoms floating around in space. Does this pose any errors in the structure or is it okie to ignore it.? Thanks. =)
Hi,
I want to model circular permutation together with domain insertion for my protein. Can anybody tell how can I do this using rosetta 3.2 ??
Thanks in advance
Dear Rosetta users,
I have created the missing domain of an X-ray structure by homology modeling and I would like to refine only this part. Is there an easy way to define a residue range in Rosetta and restrict relaxation to these residues rather than writing my own constraints file that includes only atoms from the experimentally derived part? If not what kind of constraints should I impose to the experimentally derived part of my protein (distance, dihedral, etc.)?
thanks in advance,
Thomas
I was installing rosetta 3 on Ubuntu 10.04 LTS with GCC 4.3,the compilation using 'scons bin mode=release 'went smoothly,and the 'scons cat=test' also went well,however,running 'test/run.py' ended up with a success rate of only 41% .Acutally I will be doing a little bit of development work with rosetta,so I decide it's better to find out what's keeping me from getting a success rate of 100%.Anybody got an idea?
Hey, I was testing the enzyme design application with the files (1a91_CHGW_d1_mod.pdb, D2N_aX.params, D2N_ax_confs.pdb, Est_CHba_d2n.cst and flags) provided in one of the test folders.
Here is my command line:
/usr/local/rosetta3.2/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ -overwrite @flags > enzyme_design.log
The run stopped a few seconds after it started. Here is the short log file:
core.init: Mini-Rosetta version exported from unknown