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problem with modelling of protein (140 and 150 residues respectively)

Submitted by krlitros87 on Wed, 2014-10-22 09:39
Category: 
Structure prediction

Hello everyone,
i'm having some problems with 2 proteins that have 140 and 150 residues respectively.
By now i have generated only 1000 models (i intend to create 10000 in total), but i'm not having clusters at all :/
I read somewhere that the abinitio method (related to modelling) works on protein with less that 100 residues. Is that correct?
What can i do to overcome this problem?

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Rosetta 3 - Applications

What are "-nstruct" and "cluster_histogram.txt" for "clustering.py"?

Submitted by lanselibai on Fri, 2014-10-17 06:06
Category: 
Structure prediction

Hi friends,
After following

https://www.rosettacommons.org/docs/latest/cluster.html

Can I ask something about the usage and how to interpret the results?. It seems that there is not so much information on the website.

# The following is my options
-in:file:fullatom
-out:file:silent /path/to/cluster.out
-run:shuffle
-cluster:radius -1

1. How many decoys per input structure is recommended to specify "-nstruct"?

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Rosetta 3 - Applications

Syntax for the alignment file in "minirosetta comparative modeling"

Submitted by lanselibai on Thu, 2014-10-16 15:29
Category: 
Structure prediction

Hi friends,
I am confused about the syntax for the alignment file for homology modeling.

https://www.rosettacommons.org/docs/latest/minirosetta-comparative-model...

Can I ask
1) If "-cm:aln_format grishin" is specified, in the ".aln" file:

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Rosetta 3 - Applications

ab initio modelling - what to do next?

Submitted by krlitros87 on Thu, 2014-10-16 13:05
Category: 
Structure prediction

Hi everyone,
Finally i was able to create 10000 models of my 90 residues protein.
By running cluster.linuxgccrelease i got (i guess) 560 clusters:
---
Timing:
Readin:25s
Cluster: 22s
Additional Clustering: 513s
Total: 560
---
But now i don't know what to do.
According to the IsThisModelGood.pdf document, now i have to create a plot RMSD vs score, so as i don't have a crystal structure to use as a reference, i think the best idea will be to use the structure with the lowest energy, right?

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Rosetta 3 - Applications

Knowledge check on steric effects

Submitted by pachecoj on Thu, 2014-10-16 09:13
Category: 
Structure prediction

Hi,

I am doing packing on PDB ID 1UKU and looking at two solutions my code produces, one having much higher energy than the other. The only difference between them is that the conformation of one of the Tryptophan residues is different, the other 100 or so residues are unchanged.

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Rosetta 3 - General

Questions on energy oddities

Submitted by pachecoj on Wed, 2014-10-15 13:26
Category: 
Structure prediction

Hi,

I am doing side-chain packing on a fixed backbone over a discrete set of configurations. Given a set of (non-rotamer) side-chain configurations I'm using Rosetta to calculate one-body and two-body energies using the standard scoring function. I observe to things that seem strange in the two-body energies:

1) For a pair of residues sometimes the two-body energies are almost all zero except for a couple configurations. This sort of makes sense if the residues are far enough apart, but does it make sense that they are *exactly* zero?

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Rosetta 3 - General

Looking for a pdb....

Submitted by MarkW on Mon, 2014-10-13 15:45
Category: 
Structure prediction

Hi,

Sorry for the newbie question, but I'm looking for some pdb's to practice packing methodologies on. This will be packing only to start with, not design, and I'm looking for a locked backbone, ( I've seen a function somewhere in the docs for this), and just perturbing the side chains exactly like in this video http://www.youtube.com/watch?feature=player_detailpage&v=_SDHZ-jxP4o....

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Rosetta 3 - General

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

Submitted by lanselibai on Mon, 2014-10-13 10:26
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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Rosetta 3 - Applications

Use "loopmodel.linuxgccrelease" CCD to build missing residue positions

Submitted by lanselibai on Sun, 2014-10-12 09:00
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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Rosetta 3 - Applications

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