dG/dsasa , What is the exact meaning?
Submitted by Apiwat on Sun, 2014-04-13 00:38
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# decoys of silent
Submitted by fred on Wed, 2014-04-02 06:00
Hi there,
Is there any command to get the number of decoys of a silent file without necessarily extract them? I mean, is there such information somewhere (tail?) inside the silent file? This information is useful to restart an application which have been stopped in the middle.
Thanks in advance.
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score_jd2.mpi.linuxgccrelease failed
Submitted by fred on Wed, 2014-03-26 13:54
Hi there,
I was trying to score 100k decoys in a silent file using the Rosetta's score_jd2.mpi.linuxgccrelease with the command line:
> score_jd2.mpi.linuxgccrelease -in:file:fullatom -in:file:silent query_silent.out -out:file:silent_struct_type binary -out:file:silent scored_silent.out
I've got the following on screen:
...
core.pack.dunbrack: (12) Reading /cluster/apps/fred/rosetta_2014wk05/main/database/rotamer/ExtendedOpt1-5/asp.bbdep.rotamers.lib
core.pack.dunbrack: (12) Reading /cluster/apps/fred/rosetta_2014wk05/main/database/rotamer/ExtendedOpt1-5/asp.bbdep.densities.lib
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PIKAA in resfile does not mutate Cys in disulfide bond to specified residue
Submitted by attesor on Fri, 2014-03-14 07:53
Category:
Design
Hi, I used fixbb in Rosetta 3.4 to thread a sequence on a template structure. There is a disulfide bond in the template structure, say, between two residues Nr. 20 and 50. My resfile looks like this: NATAA # keep native aa but packable! ... 20 A PIKAA G ... 50 A PIKAA G ... However, in the threaded model, all mutations specified in the resfile were realized except the two cystine residues. How can I force fixbb to mutate the two cystine residues?
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pKa app is now public!
Submitted by Sergey on Mon, 2014-03-10 15:47
Hi Everyone,
Our ROSIE server now have pKa app (developed in GrayLab http://graylab.jhu.edu) open for public. Please visit http://rosie.rosettacommons.org/ for documentation and job submission.
Best,
Sergey.
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ORBITAL records in self generated .params (ligands)
Submitted by ast on Thu, 2014-03-06 07:22
Hi all,
how do I get the ORBITAL records (that can be found in predefined normal AAs .params)
for a self generated ligand?
The molfile_to_params.py does not seem to cover that?!
thanks
ast
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ddg monomer vs pmut scan
Submitted by dave on Tue, 2014-03-04 10:18
Hello,
I'd like to predict effect of a mutation on a protein stability. I found two different applications - ddg monomer and pmut scan and I'd like to ask what is the difference between them? Are there any applications where one of them is better to use?
Dave
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smoothly kill a mpirun process
Submitted by fred on Tue, 2014-02-18 06:06
Hi there,
Sorry about this, perhaps, off topic question. The problem is I´m running a MPIRUN loop modelling processes, which I've asked for 500k decoys. Well, i've changed my mind and decided to stop it before end. I'm afraid, however, that an abrupt interruption will damage my big silent file. So, is there any way to smoothly kill such a process?
Thanks in advance.
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Relaxation with PyRosetta
Submitted by peony on Sat, 2014-02-15 04:36
Hi,
I would like to relax pdb structures with PyRosetta. I use commands
pose=pose_from_pdb(file_pdb)
relax = ClassicRelax()
relax.apply(pose)
but I have received the information about memory protection violation. Why is it happen and how can I relax my structures?
Problem solved !
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Interface energy vs binding energy
Submitted by Apiwat on Wed, 2014-02-05 00:47
Hi all,
I know, there is a little bit difference between interface energy and binding energy in protein docking.
Interface energy come from, separate 2 chain (same pose) far away and then calculate total energy
Interface energy= (complex total energy) - (separated total energy)
Binding energy com from , calculate total score for each individual chain (different pose)
Binding energy = (complex total energy) - [ (individual chain 1 total energy) + (individual chain 2 total energy) ]
right ?
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