I am trying to use FloppyTail to determine a C-terminus tail structure of 6 consecutive His residues. However, several residues before the tail also experience conformation change though the majority is remained the same. Can I ask is there a way to only optimise the tail structure?
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I am trying to use the loopmodel ccd to build a loop region with missing residue positions in the original PDB file.
The whole sequence is of 228 amino acid and the missing region is 223-228.
Can I ask
1) As the loop to be built is at the end of the sequence (i.e. termini), how can I specify the loop file?
If I use "LOOP 222 228 0 0 0", I was told (ccd_1.log attached):
"core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch"
I am trying to use "clustering.py" but I was told "OSError: [Errno 2] No such file or directory". Can I ask how to solve this?
I am sorry but it seems I have been asking technical questions all the time. Please tell me if there is something I can read to prepare my knowledge to debug. For example, how can I actually debug this python problem based on the error message?
Thank you very much.
The following is the command line and prompt.
Is there any support in rosetta for writing out a PDB file with multiple configurations of the side-chains? I have a set of side-chain hypotheses at each residue along a fixed backbone and would like to visualize this as an ensemble. This is analogous to dumping a PDB file with a side-chain at every rotamer location in the Dunbrack rotamer set.
I think I know how to implement this from scratch, but if there is any built-in support along these lines that would be great.
I've been working on a homology model of a spanning helical membrane protein. The options I'm using seem to work for a somewhat similar protein, so I can't figure out what the problem is. Essentially, the problem with the decoys is two fold:
I have a couple of questions regarding Rosetta clustering and Calibur and I wasn't able to find an answer to them on the site
Which type of clustering algorithm is used in Rosetta clustering? EDIT:I meant to ask- when calculating the RMSD is the superimposing done pairwise in Rosetta clustering?
I'm interested in Pyrosetta
and learning the tutorial
Workshop #4: PyRosetta Folding
11. Create a new subroutine in your folding code for an alternate random move based upon a “fragment insertion”. A fragment insertion is the replacement of the torsion angles for a set of consecutive residues with new torsion angles pulled at random from a fragment library file. Prior to calling the subroutine, load the set of fragments from the fragment file:
fragset = ConstantLengthFragSet(3)
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: