pair energies across interface
Submitted by irini on Fri, 2012-02-10 09:17
Hi,
How to generate the table "Pair energies across interface" in the output pdb file?
Thanks,
Irini
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Cannot get PyMOL_mover to work on MacOS
Submitted by cno on Fri, 2012-02-10 07:24
I've trying to set up the PyRosetta PyMOL viewer on a MacOS 10.7.3, 64 bit system, but I cannot get PyRosetta to send graphics(?) to PyMOL. The current setup is:
PyRosetta 2.011 [r46035]
Python 2.7.1
PyMOL 1.5.0
I start PyMOL:
PyMOL>cd /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/
cd: now in /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit
PyMOL>run /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/PyMOLPyRosettaServer.py
PyMOL <---> PyRosetta link started!
at 127.0.0.1 port 65000
Running through the walkthrough in Baugh et al I get:
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RosettaDesign Server, reproducing optimized interface conformation
Submitted by AlexanderMetz on Thu, 2012-02-09 10:41
Dear all,
I used the Rosetta Design server (http://rosettadesign.med.unc.edu) to search for mutations that stzabilize a protein-protein interface.
I have a two questions about this:
1) Is there any controll on the process, e.g., by means of a .res residue file, as is for the structure stabilization procedure? I seems like the settings in the .res file to not influence the PPIface stabilization procedure at all.
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protein-protien docking with uniform trans
Submitted by lkingsle on Thu, 2012-02-09 07:19
Hello All,
I am attempting to dock two proteins and we have a general idea of the binding site on one of the proteins (protein 1) , but are unsure where the binding site of the second protein is (protein 2). We'd like to restrict the dockable area of protein 1 while leaving protein 2 unrestricted. I am trying to use the uniform trans flag. I did some testing/internet searching but I can't seem to understand exactly how its working. Here is the definition:
Uniform random repositioning of the second partner about the first partner within a sphere of the given radius, [R].
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Difference between relax and mimimize_with_cst
Submitted by basvandenberg on Thu, 2012-02-09 00:16
Hi all,
Reading the documentation of the ddg_monomer application I noticed that minimize_with_cst is needed to reduce collisions that result in a high free-energy score. For some structures I already used the relax application to achieve this. Hence my questions:
1. What does minimize_with_cst do? And how does it differ from what the relax application does?
2. Can I use my relaxed structure as input to a low res ddg_monomer run?
Looking forward to hear from you.
Cheers,
Bastiaan
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parameterizing new residues
Submitted by chiendarret on Fri, 2012-02-03 22:59
Aim: ab-initio protein-modeling-docking for proteins containing non-standard amino acids .
I was able to parameterize the new amino acids for Amber ff, which developed along QM calculations for also K-Br atoms, i.e., at higher level than 6-31G* and DFT in place of HF. It worked: the MD simulation showed protein stability along 15 ns by using a NAMD-CUDA cluster.
Then, I collected info from Rosetta.3.3 forum, especially about mol2 file -> Rosetta parameters, such as in the thread initiated by einew on 02/28/2011 on "Rosetta applications".
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New files for loop modeling
Submitted by Victor on Fri, 2012-02-03 14:36
Hi,
I have a question about new files for loop modeling - 650_LoopsKIC.py and T660_LoopBuilding.py .
I need generate N decoys and get N pdb files, and score them. How to implement these new files for that.
Do I need fragment files for loop generation if I use these files, like for old loop_modeling.py?
Unfortunately I did not find any reference for that.
What new features they have compare with loop_modeling.py ?
Thank you, Victor
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option removal/KIC
Submitted by jadolfbr on Thu, 2012-02-02 16:35
Is there any way to remove options during a script once initialized in rosetta.core.init( args )?
-J
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Changing Monte Carlo temperature for relax
Submitted by jruhym on Thu, 2012-02-02 15:18
If relax has MC as part of its procedure, is there a way to change the kT value in order to allow it to select more (or less) aggressive conformational changes? I don't see any flag/switch/option for this.
Thanks in advance for your help.
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error during docking
Submitted by zhisheng on Thu, 2012-02-02 12:10
Hello,
When I start running docking calculation (docking_protocol.linuxgccrelease), there was an error:
ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1290
The command I used (just for test)t is:
dock -in:file:s ./prepack_protein.pdb -in:path:database $database -docking:docking_local_refine 1 -docking:dock_pert 3 8 -docking:spin 1 -docking:dock_min 1 -docking:partners [A_B] -docking:sc_min 1 -nstruct 50 -ex1 -ex2 -out:path:pdb ./path/ -out:file:scorefile ./path/
What's the problem? Or the prepack pdb file?
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