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The design of a helical peptide

Dear Rosetta developers,

I am interested in the de novol design of a peptide with helical conformation which could bind a specific protein partner with enhanced affinity. However, when consulting the user guide, i lost my way about the specific method. So could you be so kindly to tell me which method or module in Rosetta can do such kind of case , or provide me a step-by-step guidance.

What i intended to do was listed in the following:

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spline constraint

I havn't been able to find an example of the spline constraint histogram there an example somewhere that I missed?

Also, within the constraint code, is it possible to give an already-generated spline to use for the constraint? What are the requirements of the spline (bicubic, tricubic, etc)?


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How to do the testing job for Rosetta 3.4 ?

Hi everyone,

I am trying to install Rosetta 3.4 on CentOS release 5.5. I built the Rosetta executables with the command "scons bin mode=release" according to the user guide . However, i lost my head for how to do the testing jobs. I searched through the forum and it seems that i should do the unit test firstly and then try the integration test. So my first questions is whether this testing routing make sense.

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postive score models from AbinitioRelax

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:

-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
-nstruct 10
-use_filters true
-psipred_ss2 ./t000_.psipred_ss2
# -kill_hairpins ./t000_.psipred_ss2
-abinitio::increase_cycles 10
-abinitio::rg_reweight 0.5

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Dock antibody at the epitope of antigen

Deal all:

I am a beginner of computational protein docking. For my current project, I am going to dock Ab at Ag using PyRosseta.
Is there any option or parameters that I can constrain the region (epitope) of Ag to be docked by Ab? I would like to extract the value of scoring function based on this constrain (epitope).

Please having your comments or suggestions regarding how to do that.
Thanks so much,


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"Problem in calculating overlap between atoms" error occurred in Point Mutant Scan application

Hi all,

I'm trying to run pmut_scan_parallel application with "-score:weights design_hpatch.wts" scoring function, as suggested in manual. However, it always exits from: src/core/scoring/ line 215 and an error reported:

"Problem in calculating overlap between atoms. Termination calculation.
radius_a: 3.16, radius_b: 3.16, distance_ijxyz: 14.199, cosine theta: 2.245"

Does it mean that atom a and b are too far from each other so that there is no overlap between them? Why it happens in hpatch scoring, and any suggestion to avoid it?

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