The problem hasn't been solved
Dear friends,
I am not sure what is wrong with the flag "-l" for score_jd2.linuxgccrelease. When I use:
~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -l /mnt/hgfs/Downloads/PDBLIST.txt
I got prompt:
Dear friends,
Can I ask the syntax to build a silent file?
1) My purpose is to create a silent file based on all the PDB files in /mnt/hgfs/Downloads/
I am trying:
~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:s *.pdb /mnt/hgfs/Downloads -out:file:silent /mnt/hgfs/Downloads
After several prompts, I got the error of
Dear friends,
After obtaining multiple (e.g.100) models from relax.linuxgccrelease, I think I need to select the most likely one for further design work. By looking at
2) Is this Model Good.pdf
3) Preparing Your Structure.pdf
in Meiler Lab's tutorials, I think I need to do "cluster model" and "score vs RMSD plots" to determine the best model.
I can find cluster protocol in
https://www.rosettacommons.org/docs/latest/cluster.html
Dear Friends!
I am new to rosetta and I would like to become proficient in running it. As a start I need to find out if it is feasible to force disulfide bonds on the N and C terminal of a protein that does not have any disulfide bonds in nature but will be relevant for fusing into another protein structure that forms disulfide bonds such as the fusion occurs at the disulfide bond branch. My template sequence and target are of different length and so i ran into the this error
"core.conformation.Conformation: [ERROR] Residue 246 is out of range."
Hi everyone,
I just compiled rosetta (2014.20.56838_bundle) on a cluster with Centos, using the following command:
./scons.py -j16 bin
Under Residue.chi() there is a warning
CAUTION: This function does not cause updating to any internal coordinate data. See Residue::set_chi() and Residue::set_all_chi() functions for versions which handle coordinate updates.
But in code it seems that Residue::set_chi() and Residue::set_all_chi() (at least in pyrosetta) do not update internal data as well. Is this a bug or a feature?
What is the most elegant way to display rotamers in PyMol?
This is a spin-off from this question.
I have a basic implementation working here. I had the most problems since doing r.pose_from_sequence('Z') was not working.
Any suggestions about improving this are welcome.
_______________________
def display_rotamers(pose, rotamers, pymol_mover):
Dear friends,
I am trying to use relax.linuxgccrelease to remove any clashes in my PDB file.
Can I ask
1) As I understand from "3) Preparing Your Structure.pdf" in the "introduction" tutorial from Meiler Lab, I should use
relax.linuxgccrelease -database <database> -s <structure> -ex1 -ex2 -relax:sequence -nstruct 100
However, I have been told that:
ERROR: Unused "free" argument specified: -database
I saw the talaris2013.wts have mentioned that "the 05.2009 ideal coordinates for # the amino acids". May I ask what is 05.2009 ideal coordinates? Where can I find the document for this coordinates standard？ Thanks
Hello,
I am trying to dock a single helix onto a specific region of a protein. When running a docking simulation using Pyrosetta the helix moves to another site on the protein. Is it possible to only allow the helix to explore a certain region of the target protein?
Many thanks in advance,
Alexander