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

[Anonymous]

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”?

2. The following is the content of “cluster_histogram.txt”, how to interpret this?

(line 1) bin 0 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.25 2.5 2.75 3 3.25 3.5 3.75 4 4.25 4.5 4.75 5 5.25 5.5 5.75 6 6.25 6.5 6.75 7 7.25 7.5 7.75 8 8.25 8.5 8.75 9 9.25 9.5 9.75 10 10.25 10.5 10.75 11 11.25 11.5 11.75 12 12.25 12.5 12.75 13 13.25 13.5 13.75 14 14.25 14.5 14.75 15 15.25 15.5 15.75 16 16.25 16.5 16.75 17 17.25 17.5 17.75 18 18.25 18.5 18.75 19 19.25 19.5 19.75

(line 2) count 485 948 724 933 1120 669 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Thank you very much.

Yours sincerely
Cheng

[Anonymous]

The cluster application doesn’t generate any new structures, it just processes existing ones (one-in/one-out), so -nstruct doesn’t really make sense for the clustering application.

The histogram that Rosetta clustering produces is the histogram of pairwise similarity values for the initial clustering set. That is, when it does the inital all/all distance matrix, how do the rmsds distribute themselves. In your case, there were 933 structure pairs that had rmsds between 0.75 and 1.0 Angstroms.

[Anonymous]

Hi R Moretti,
Thank you.

1) On the website of

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

The flag -nstruct does exist. So is it incorrect?

2) Thank you for your explicit explanation for the histogram. I got it now.

Yours sincerely
Cheng

[Anonymous]

-nstruct is indeed one of the “general file IO options common to all Rosetta applications”, but in the case of cluster it actually doesn’t do anything. (I’ll fix the documentation – thanks for pointing that out.)

[Author]

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