Is it CS-HM Rosetta restraint derivation i.e cm_scripts in Rosetta 3.3 bundles?

[Anonymous]

Hi,

Can someone point me to the location of cm_scripts in Rosetta 3.3? It seems like I couldn’t find it in rosetta3.3_bundles. Please also let me know if it is located in greater versions.

Also how to configure several options in the file cm_scripts/rosetta_cm.conf? There is no detail instruction in CS-HM Rosetta paper.

Thanks in advance for the information.

[Anonymous]

cm_scripts wasn’t released at the time (and actually hasn’t been yet). A different user pointed out this oversight recently. It’s on my to-do list after we get 3.5 out and weekly releases started – tentatively end of April?

Here’s an “example conf” I found in the developer cm_scripts, does it help any? I can get James’s attention if you need it…it will probably be helpful for us to release cm_scripts first.

# Listing of default options for setup_cm.pl.
# Lines beginning with # characters are ignored.
boinc_tag rosetta_cm
method loopbuild_threading_cst_relax

# alignment filtering options
max_templates 20
max_pct_id 1.0
max_template_pct_id 1.0
max_e_value 10.0
# date cutoff of 0 means don’t filter based on date at all
date_cutoff 0

#erase the following line to not use hhblits
#use_hhblits

# paths for external programs
mini_path /work/tex/src/rosetta/rosetta_source/bin
mini_db_path /work/tex/src/rosetta/rosetta_database
mini_compile_mode release
mini_compiler gcc

nr_db /scratch/shared/genomes
hhsearch_path /work/tex/hhsearch

[Anonymous]

We can’t distribute HHsearch – that’s why there’s an hhsearch_path in the config file, so you can set the path to wherever you installed it for yourself.

[Anonymous]

Many thanks for your response.

Actually I need these cm_scripts very soon for some of my experiments. Is it possible to release it in the beginning of April?

Thanks for listing the “example conf”. It must be useful to run the cm_scripts I believe.

One thing, I installed and configured HHsearch in my local server. But the latest database (pdb clustered around 70% seq. identity) that I downloaded from the HHPred ftp server seems to be corrupted. Does cm_scripts bundle come with HHsearch executables and databases?

Thanks a lot!

[Author]

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