The problem hasn't been solved
I could not find instructions on PyRosetta site or this forum on how to read in a silent file so I can obtain a set of poses at once. It is not in the FAQ, either. Or should I always extract_PDBs from the silent file first ?
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:
Can one consider prepack before docking as a fast relax of subunits with backbone constraints?
If so, can one replace prepack step with a fast relax with backbone constraints of subunits?
I havn't been able to find an example of the spline constraint histogram format...is 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)?
-Jared
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.
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/d...
-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
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,
Hsih-Te
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/sasa.cc 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?
Hi,
How can I incorporate backrub motions in the DDG Monomer sampling protocol? Are those already taken into account when using the High Res protocol (16 in Kellog's article)?
Since now a week the antibody server at http://antibody.graylab.jhu.edu/ is not accessible.
Is there a possibility to use the antibody server on http://rosettaserver.graylab.jhu.edu/antibody/submit instead? Is it the same as the other one or is it really a 'new' developement?
Or is there a possibility to make the first server work again? (to who, do I have to address for this issue?)
Thank you all for your efforts with the rosetta software suite.
