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.

[Anonymous]

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.

[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

[Anonymous]

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.

[Author]

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