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Structure prediction

How to only constructure the tail conformation when using "FloppyTail.linuxgccrelease"?

Category: 
Structure prediction

Dear friends,
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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Use "loopmodel.linuxgccrelease" CCD to build missing residue positions

Category: 
Structure prediction

Dear friends,
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"

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"OSError: [Errno 2]” in “clustering.py”

Category: 
Structure prediction

Dear friends,
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.

Yours sincerely
Cheng

The following is the command line and prompt.

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Write PDB with multiple side-chain configurations

Category: 
Structure prediction

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.

Thanks,
Jason

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Membrane homology modeling loop building gives very strange outputs

Category: 
Structure prediction

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:

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clustering

Category: 
Structure prediction
Design

Hi,
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?

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I don't know what's the problem when load the fragment file

Category: 
Structure prediction

Hello ~
I'm interested in Pyrosetta
and learning the tutorial
Workshop #4: PyRosetta Folding
page 4
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)

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Some wrong with the flag "-l" for score_jd2.linuxgccrelease

Category: 
Structure prediction

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:

Post Situation: 

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