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Trouble enforcing a disulfide in loop building

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Trouble enforcing a disulfide in loop building


Like some others on this forum, I'm having some trouble getting disulfides to work. I pass

-in:fix_disulf ./disulf

where disulf is a text file containing the residue numbers of the cysteines I am trying to bridge like so:

269 280

With an empty line at the end, which others have mentioned may be necessary. Unfortunately, this has no discernable effect on the loop in question--I have done pretty extensive testing, and I never see a disulfide form. Should I try to encode this disulfide as a constraint, or is there something I'm clearly doing wrong?


Given that -in:fix_disulf has no effect by my lights, can any of you suggest a benchmark or standard to test whether this command is working properly in my installation? I've had success with other projects, so it would have to be a pretty specific issue.


Post Situation: 
Sun, 2015-05-10 16:31

-in:fix_disulf (note the underscore and not a colon between fix and disulf) is handled at the application level, rather than at a general Rosetta level - depending on your protocol it may not even be read. Which protocol are you using?

If your protocol does not obey -in:fix_disulf, then (atom pair) constraints may be the way to go - many protocols, even if they don't obey -in:fix_disulf, will automatically detect disulfides if the two cysteines are close enough.

For an example of -in:fix_disulf usage, you can take a look at Rosetta/demos/protocol_capture/2012/replica_docking/, which makes use of it.

Mon, 2015-05-25 11:56

Looking back at what I've done, I was passing -in:fix_disulf with correct punctuation, I just reproduced it incorrectly in my first post.

I'm using a homology modelling protocol to do loop building on a membrane protein, here's the contents of the options file:

-s ./hTRPM8_full_c-term_threaded.pdb
-loops:loop_file ./test.loops ##loop file
-loops:extended true
-loops:relax fastrelax
-ex1 #Include extra chi1 rotamers
-loops:frag_sizes 9 3 1
-loops:frag_files ./aat000_09_05.200_v1_3 ./aat000_03_05.200_v1_3 none
-loops:remodel quick_ccd
-loops:refine refine_kic
-in:file:psipred_ss2 ./t000_.psipred_ss2
-in:file:spanfile ./modellerrebuild.span
-in:file:lipofile ./hTRP.lips4
-in:fix_disulf ./disulf
-score:weights /usr/local/apps/rosetta/rosetta-3.5/rosetta_database/scoring/weights/membrane_highres_Menv_smooth.wts

Any idea what the problem might be? I've begun to try using an atom pair constraint, we'll see how that goes.

EDIT: For anyone with similar problems, I seem to have successfully generated disulfides by passing this constraint file:

AtomPair SG 269 SG 280 HARMONIC 1.800 2.05

with these options:

-cst_fa_file disulf.cst
-cst_fa_weight 1000

Wed, 2015-05-27 14:36