empty dir rosetta_source/src/apps/pilot
Submitted by Anonymous on Thu, 2012-06-14 08:28
I run Rosetta 3.4 on Ubuntu 12.04 64bit. I could no find program remodel after installing v3.4.
Post Situation:
Forums:
You are here
Unsolved
The problem hasn't been solved
force point mutation with fixbb
Submitted by Anonymous on Wed, 2012-06-13 09:15
I have run relax on a protein of ~100 aa (Rosetta 3.4). All residues show score below 0.0 except one LEU:
label fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref total
LEU_27 -3.80035 0.405712 0.674211 0.0228272 0 0 0 0 0 0 0 0 0 0 0.972498 0.171944 1.80864 0.319658 -0.1 0.475143
Post Situation:
Forums:
Fold and Dock - chains not in contact
Submitted by arthuc01 on Wed, 2012-06-13 01:45
Hi
I wonder if anyone can suggest a solution, I am attempting to perform a fold and dock calculation. however, in about 80% of the structures generated by Fold and Dock the chains are not in contact with one another. On top of this, in about 5% of the cases I have actual overlapping of the structures (eg a helix (Ca not just side chains) will exist in the same position for each monomer)).
The command I am using can be found here
Thanks for your help
Post Situation:
Forums:
Fragment File Reading problem
Submitted by Nuria on Tue, 2012-06-12 13:42
Biopython error in mac os x
Submitted by vinodh on Tue, 2012-06-12 12:23
Hi,
I am new with mac osx and rosetta. I have rosetta 3.3 installed and have trouble with installation of biopython 1.59. on my mac os 10.7, have already installed Xcode 4.3.2. I have pasted the error message. Any help would be highly appreciated.
Thanks
$cd biopython-1.59
$sudo python setup.py install
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-intel-2.7
creating build/lib.macosx-10.7-intel-2.7/Bio
copying Bio/__init__.py -> build/lib.macosx-10.7-intel-2.7/Bio
copying Bio/_py3k.py -> build/lib.macosx-10.7-intel-2.7/Bio
.
.
Post Situation:
Forums:
about Residue Number in Rosetta
Submitted by jiongzhang on Mon, 2012-06-11 14:58
Does Rosetta use the residue number written in the pdb files? Or it just take the first shown residue has the residue number 1?
I need to clarify this issue so that the constrains are applied correctly.
Thank you very much.
Post Situation:
Forums:
input_score_filter not taken by program cluster ?
Submitted by Anonymous on Mon, 2012-06-11 09:14
Hi, I have Rosetta 3.4 here.
When I run cluster using parameter -cluster:input_score_filter , it seems to me the parameter is just ignored and all decoys (no matter its score is higher or lower than the limit) are considered. I got the same results no matter I set the parameter or not. I read the source file at rosetta_source/src/apps/public/cluster.cc and it seems variable input_score_filter is not used (together with some other parameters). Function GatherPosesMover::set_filter in rosetta_source/src/protocols/cluster/cluster.cc seems never invoked anywhere.
Post Situation:
Forums:
Trouble building rosetta3.4 on Mac OsX 10.5.8
Submitted by jspegman on Sat, 2012-06-09 07:31
I have unpacked all of the files but each time that I enter scons bin mode=release I keep getting this read out:
josh-spegmans-macbook-pro:rosetta_source joshspegman$ scons bin mode=release
scons: Reading SConscript files ...
Running versioning script ... sh: git: command not found
Done. (0.1 seconds)
scons: done reading SConscript files.
scons: Building targets ...
Post Situation:
Forums:
what is the F() in rosetta 2.3
Submitted by Lindsay on Fri, 2012-06-08 14:44
Dear ALL,
When I was looking the energy score printed in the make_pdb.cc file, I found there was code like
iunit << A( 15, "score:" ) << F( 11, 2, score ) << '\n';
What is the F()? Thank you!
Post Situation:
Forums:
Docking.py - protocols.docking.DockingInitialPerturbation: moving together failed. Aborting DockingSlideIntoContact.
Submitted by pepfolder on Fri, 2012-06-08 13:56
When I run the docking script, it starts out ok, but, as the run progresses, the ligands are being placed further and further from the target substrate. Also, I get the message "protocols.docking.DockingInitialPerturbation: moving together failed. Aborting DockingSlideIntoContact."
Is there any way to constrain where the movers will place the ligands? I'm using the following command line options:
docking.py --pdb_filename hard_to_dock.pdb --partners AB_C --jobs 1000 --job_output docked --translation 3 --rotation 8 --PyMOL_Mover_ip off
Post Situation:
Forums: