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How to insert a TER line between docking partners

Submitted by devroop on Sun, 2012-07-29 13:48

Can anyone please help regarding how to insert a TER line between docking partners (in the pdb of the docked complex)? Actually, I have the pdb file of a docked protein-protein complex(generated by a global docking platform). Now I need to prepare the input file (pdb) for a local docking search using Rosetta. So I need to insert a TER line between the docking partners.

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Rosetta 3 - General

the energy terms in fixbb

Submitted by tianbu on Sun, 2012-07-29 12:48

Dear developers,
It says in rosetta2.3 manual
“The main score is Wbk_tot * bk_tot + Wother * other. The other terms that contribute to the score evaluate the backbone stucture, e.g. the ramachandran score. The score is supposed to be the energy with bk_tot as just one part of it. For the sake of consistency, the score can be used instead of bk_tot when thinking of the quality of output structures”
Can anyone tell me what are the other terms in the fixbb scoring function? Thank you!

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Rosetta++ - General

Does any paper descript rosetta2.3's scoring function (fixbb )

Submitted by tianbu on Fri, 2012-07-27 14:50

Dear developer,
Does any paper descript rosetta2.3's scoring function? I am confused by the scoring function in rosetta2.3 and rosetta3.3. Does them share the same energy terms and weights? Or where can I find out all these information? Thank you very much!

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Rosetta++ - General

Rosetta 3.4 build on Fedora 16 (VM)

Submitted by Ryhon Wang on Fri, 2012-07-27 01:06

Dear All,

I am trying to build Rosetta 3.4 on Fedora16 when I type ./scons.py bin mode=release at command line.

./scons.py bin mode=release
scons: Reading SConscript files ...
Running versioning script ... svn: “.”不是工作副本
Done. (0.0 seconds)
scons: done reading SConscript files.
scons: Building targets ...

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PyRosetta - Build/Install

Flexible backbone design using PSSM

Submitted by kalicuta on Thu, 2012-07-26 13:38

Hi,

Currently I am running Rosetta flexible backbone design (ver. 3.3) to create novel proteins. My problem is, when I add PSSM as a favourable sequence profile, sometimes negative/positive weights behave strangely. The below is my XML code.

[Reweight scoretype=res_type_constraint weight=1.0/]

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Rosetta 3 - General

RosettaVIP: ERROR: seqpos <= size()

Submitted by Anonymous on Thu, 2012-07-26 07:30
Hi, I tried RosettaVIP shipped in Rosetta3.4. In some cases it breaks after a few iterations with this error: ERROR: seqpos I can not figure out the root for the error from the source file. The command line I used is: vip.linuxgccrelease -s mypdb -cp:cutoff 6.0 -sasa_calculator_probe_radius 1.0 -cp:output myoutput -cp:print_reports -run:silent I have not observed other anomalies in the screen printout before the ERROR, neither in the reports.txt file.
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Rosetta 3 - Applications

problems with low-resolution loop refinemet (LoopMover_Perturb_CCD)

Submitted by aloctavodia on Thu, 2012-07-26 06:51

Hi,

I am trying to replicate some of the examples of the PyRosetta manual and tutorial. I have several problems with the LoopMover_Perturb_CCD. See the code below

1) I am getting the same conformation 10 times (instead of 10 different conformations). Conformations looks the same and have the same energy. Is LoopMover_Perturb_CCD not properly working in PyRosetta or what I am doing wrong?

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PyRosetta - General

how to repacking loop while freezing other residues?

Submitted by jfhuang on Wed, 2012-07-25 06:59

Hello,

I rebuilded two missing loops in a crystal structure and tried to use Rosetta to refine these loops. I want to refine the loops but keep the rest of the native structure (both backbone and side chain) "freeze". However,each time the loops were repacked, the neighbor residues connect to the loops will also move. I tried to fix the native structure with -loops:fix_natsc, and also try to set the neighbor distant to 0, but all failed.

The command was:

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Rosetta 3 - Applications

How to import SymmDock models into Rosetta for local docking and energy minimization

Submitted by devroop on Fri, 2012-07-20 13:20

We are dealing with a gap-junction protein which forms a hexamer of identical subunits. Now, we want to dock the subunits into a hexamer to examine the overall complex structure. Initially we have created models of docked complexes of our protein on the Symmdock server. Now we want to import the Symmdock models into RosettaDock server for a local docking search. Please help rearding how to import SymmDock models into Rosetta for local docking search and energy minimization

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