Reply To: is it possbile to cluster pdb files?

[Anonymous]

> Hello:
> I found that rosetta could cluster the PDB files generated by rosetta itself(it generate information for PDB file which would be used during cluster). I have t thousands of PDB file generated from other program, and I am wondering is it possible for Rosetta to cluster them?
> Thank you very much.

Dear:
It doesn’t work. It is said:

ERROR: ERROR:: Unable to open silent_input file: ‘folding.silent.out’

I used the cluster protocol as following:

-cluster
-radius 7
# default clustering radius is 3A
# fiddling with the radius is the simplest way to vary the clustering
#-input_score_filter 100
# exclude structures above a given energy (in Rosetta Energy Units)
#-limit_clusters 5
# only retain largest N clusters
#-remove_highest_energy_member
# remove putative outlier from each cluster

-in
-file
-silent folding.silent.out
-fullatom
# the clustering executable accepts a set of pdbfiles, (-s *pdb)
# a file containing a list of pdbfiles, or
# a silentfile containing multiple structures
#-native 1ubi.pdb
# you may optionally include the native structure if it is known
# for benchmarking purposes. It will calculate CaRMSD from native.
-path
-database /soft/rosetta3.1/database/
# edit this path to point to your rosetta3 databases

-out
#-prefix aa
#
#-path output # path where PDB output files will be written to, default ‘.’
# if you specify a directory name here, it must exist
#-nooutput # suppress output of pdbfile structures

-mute core.util.prof # don’t show timing info