The problem has been solved
Dear all,
I'm trying to using rosetta to execute following protocol:
aa t000 _ -relax -looprlx -nstruct 10 -fa_input -use_sspair -random_loop -termini -idl_no_chain_break -loop_skip_rate 0.0 -vary_omega -l pdbs.list
but after creation of 1-7 on 200 decoys roserra crash with this error:
WARNING: pose::set_fold_tree reordering tree at 1
bad fold tree!
jadolfbr, 2013 - Please do not use this GUI. It was a beta version of an expanded PyRosetta Toolkit GUI which should be released in Rosetta Version 3.5.
Hi All. Just wanted to share part of an application that I've been working on. It is a Tkinter application for use with Minimization of Proteins and Loops.
It uses the Rosetta Classic Relax, Fast Relax, dfpMin Minimization, and Sidechain movers.
Run it using "python Tkinter_Min_main.py" (All files need to be in the same directory, and the extensions changed to .py)
I've been using the PyRosetta JobDistributor which should allow you to launch many instances of the same script in parallel, and each instance will work on a different decoy. Thus, for your N decoys each instance will work on approximately N/m of them, where m is the number of individual instances of the script you run. I have been running on our cluster, and noticed that after launching say a dozen instances of the script, after a number of minutes, some instances would start dying. After a few more minutes, I'd be down to only a few instances still running.
Well I have run AbinitioRelax.linuxgccrelease for the first time and had it produce a t000_silent.out file. The documentation says to use score.linuxgccrelease but that no longer exists in rosetta 3.2. What do I need to do to get .pdb files from the silent output file? Thanks.
I just got Rosetta 3.2 built on linux and I'm trying to run abinitio for the first time. I am getting this error when I run AbinitioRelax.linuxgccrelease.
ERROR: [ERROR] Unable to open kill_hairpins file
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 344
I would like to use new functions introduced in PyRosetta2.0 (based on Rosetta3.2).
How and where can I find such functions and make them run?
For example, when I try to run "matcher" application and "comparative modeling" application how can I find/set commands and options for them in PyRosetta2.0?
I see folders named "comparative_modeling" and "match" in the build/rosetta/protocols folder.
I am running PyRosetta on Windows XP. I have never run Rosetta3.2 on the same machine because the compilation using cygwin/MinGW is not done properly.
Any information would be helpful.
Hi
I am trying to run the make_fragments.pl script from rosetta 3.2. But it seems that I don't have the sam.predict-2nd file for sam secondary structure predictions. If anyone could send me the file and how to install it, I would be highly grateful.
Hi
I are there any tutorial or comment constrains file available. I have been unable to find any in the documentations. What I am particular is looking into is make a constrain between the cofactor and the ligand.I would be happy to see any constrain files that are available for the public. There was a set of good tutorial at Meierlab but it seems that they have removed them. A good example would be to have a distant between the Oxygen and the iron of hemoglobin.
Knut J
I've got an error while I am running the following command:
/soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abi nitio/run_lips.pl test.ali test.span /usr/bin/blastp /home/albert/softbake/biosoft/rosettadb/nrdb /soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abinitio/ alignblast.pl
error:
Error in alignblast.pl: blast output file test.ali truncated:
readline() on closed filehandle MSA at /soft/rosetta-3.2/rosetta_source/src/ap ps/public/membrane_abinitio/run_lips.pl line 91.
could you please tell me how to solve this?
THX
Windows version of PyRosetta 2.0 is ready for download. Please see our web site (http://www.pyrosetta.org/) for details and download link.