- This topic has 6 replies, 4 voices, and was last updated 13 years, 3 months ago by Anonymous.
July 28, 2010 at 8:45 am #640Anonymous
I’m using Rosetta 3.1 fixbb and would like to monitor the residual SASA packing scores. These were automaticly printed in the PDB output of Rosetta++ design mode. Is it possible to do the same in Rosetta 3.1?
July 28, 2010 at 2:33 pm #4520Anonymous
Not out of the box. If you’re willing to get your hands a little dirty I can describe how to do it. If you don’t want to write code, then I’d suggest sticking with ++ for something as simple as fixbb (or running fixbb in 3.0, then running it through ++ with a NATRO resfile just to get sasas)
In general terms:
You’ll want to use the class protocols/toolbox/PoseMetricCalculators/SasaCalculator. This class will take a Pose and calculate the per-atom SASA. You can then query it to get per-pose, per-residue, and per-atom SASAs. Create this class in fixbb.cc near the top of main(); you can get it later with a string name based lookup from anywhere in the code (that runs later, anyway).
The second step is loading the per-residue information into the Job object, with a call like protocols::jd2::JobDistributor::get_instance()->current_job()->add_string_real_pair(resnum_as_string, sasa_from_calculator );
Where to put this call is a stickier problem – you’ll probably want to just modify the PackRotamersMover directly. Be wary that this will screw up all the other apps that rely on PackRotamersMover unless you protect it with an option somehow. You could also just create a dummy Mover and insert it into the SequenceMover seen in fixbb.cc; this would prevent changes from affecting the rest of the code but requires a little more work (nevertheless it’s what I would do.)
This will add a big stack of per-residue SASAs to the end of the output PDB. I can offer more advice if you need it, let me know.
July 29, 2010 at 11:50 am #4524Anonymous
Would these numbers be the solvent-accessible surface-area (SASA) or the packing score based on SASA as described in the Materials and Methods section in Sood & Baker, JMB 357 (2006), p.917-927. The last thing was what I was after…
July 29, 2010 at 2:30 pm #4527Anonymous
This is SASA. SASApack (which, off the top of my head, is what you’re asking about) is not available in Rosetta 3.0. SASApack was replaced with the packstat application, which does a similar thing differently.
August 31, 2010 at 1:39 pm #4589bpierceParticipant
Hi, I have the same issue, sasapack is such a useful score, but the packstat app is not available to my knowledge in the latest r3.1 release. SMLewis suggestion to use fixbb from r2.3 with -natrot works well, but my preferred way to go for now is to use score mode with the following cmd line:
rosetta.macgcc -score -fa_input -scorefxn 12 -atom_vdw_set highres -find_disulf -decoystats -scorefile score12 -fa_output -nstruct 1 -no_optH -s
The -no_optH is important to score the identical structure without any atoms changing before/after the scoring. Even if you use fixbb for scoring, you should still use this flag.
September 1, 2010 at 3:03 am #4590Anonymous
Yes, you can use packstat score in Rosetta3.1 like this:
protocols : : moves : : PackStatMover psm;
But I am looking forward using RosettaHoles/2. The current 3.1 package missed external program specified by the option -dalphaball. I guess it is a 3rd party program to calculate vol of balls. Which program shall I choose to configure?
September 1, 2010 at 2:03 pm #4591Anonymous
dalphaball is indeed a separate program, which you’ll need to get the holes stuff working correctly. Try contacting Will Sheffler in the Baker lab if you can’t get it working.
- You must be logged in to reply to this topic.