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Structure prediction

Can I assume the outputs from different runs are from a same batch?

Category: 
Structure prediction

Dear friends,
I am using "minirosetta.linuxgccrelease" for homology modelling. It is recommended at least 1000 outputs are needed. However, after running 3 days, my PC got a problem and only ~500 outputs have been generated. If I run a second run, can I just run another 500 outputs and combine them together with the first batch outputs, and assume those 1000 outputs are generated from same batch?

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

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

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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Syntax for the alignment file in "minirosetta comparative modeling"

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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ab initio modelling - what to do next?

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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Knowledge check on steric effects

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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Questions on energy oddities

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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Looking for a pdb....

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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