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.
PDBs are PDBs, so long as they are valid PDB files Rosetta will try to cluster them. There isn't anything special embedded in rosetta-created PDBs used in clustering that I'm aware of. Let me know if it works.
> 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
Well, yes, it's failing because you haven't supplied the inputs. It's right in the commentary (marked by #) under the flag with the same name as the error message.
You need to get rid of the flag in-file-silent folding.silent.out, because you don't have that input. Instead use -s (list your pdbs on the command line) or put the list of pdb inputs in a file called pdblist and do -l pdblist.