postive score models from AbinitioRelax

[Anonymous]

I am trying to fold a protein of 140 AA in Rosetta 3.4 AbinitioRelax with the flags suggested in Rosetta 3.4 manual page:
http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d0/dd9/abinitio.html

-in:file:fasta ./t000_.fasta
-in:file:frag3 ./aat000_03_05.200_v1_3
-in:file:frag9 ./aat000_09_05.200_v1_3
-database /home/zhang/local_programs/rosetta3.4/rosetta_database/
-jran 1234567
-abinitio:relax
-nstruct 10
-out:pdb
-use_filters true
-psipred_ss2 ./t000_.psipred_ss2
# -kill_hairpins ./t000_.psipred_ss2
-abinitio::increase_cycles 10
-abinitio::rg_reweight 0.5
-abinitio::rsd_wt_helix 0.5
-abinitio::rsd_wt_loop 0.5
-relax::fast

the -kill_hairpins was excluded because the “header input” problem (see the discussion at http://www.rosettacommons.org/content/killhairpin-error). I got 8 models out of 10 with positive scores (from 416.019-2331.730, F_0000000*.pdb), two models with negative scores (-246.811 and
-244.776, S_0000000*.pdb). Is this a typical run?
Thanks!
XP

[Anonymous]

I can’t tell you if it’s typical or not.

10 structures is atypical. 10,000 structures is a more reasonable number.

140 residues is longer than suggested for ab initio. 100 is the longest that works well.

[Anonymous]

Sorry, here I just wonder if the ratio of F and S models (4:1) is typical, not the nstruct number. Which parameter could we adjust to change the ratio? Are the F models useful? If not, could we exclude (discard) them during an early stage?

[Anonymous]

Note the F versus S in the structure names, as well: Rosetta knows those F’s are failures (F for fail).

[Anonymous]

I would guess it’s atypical but I don’t run much ab initio so I can’t say. The fact that they bothered to program an automatic filter system implies that for some systems, at least, the failure rate is high enough to be a problem. I usually see something like a 1 in 5 failure rate for the sorts of things I work on.

Try -abinitio:use_filters true, -abinitio::relax_failures false, -abinitio::no_write_failures true. This may or may not improve speed (by skipping relax), it should at least stop wasting disk space on useless failures.

I don’t think F models are useful for anything but debugging.

[Author]

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