- This topic has 3 replies, 2 voices, and was last updated 13 years, 2 months ago by Anonymous.
October 6, 2010 at 9:38 am #680Anonymous
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.
October 6, 2010 at 6:12 pm #4640Anonymous
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.
October 7, 2010 at 2:10 pm #4641Anonymous
> 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.
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:
# default clustering radius is 3A
# fiddling with the radius is the simplest way to vary the clustering
# exclude structures above a given energy (in Rosetta Energy Units)
# only retain largest N clusters
# remove putative outlier from each cluster
# the clustering executable accepts a set of pdbfiles, (-s *pdb)
# a file containing a list of pdbfiles, or
# a silentfile containing multiple structures
# you may optionally include the native structure if it is known
# for benchmarking purposes. It will calculate CaRMSD from native.
# edit this path to point to your rosetta3 databases
#-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
October 8, 2010 at 1:48 pm #4642Anonymous
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.
- You must be logged in to reply to this topic.