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eval_ci_2b() with hydrogen bonds

Submitted by TensorDuck on Fri, 2018-03-30 14:05
Category: 
Scoring

I am trying to compute the residue-residue pairwise energy for several residues inside a protein structure. I found the method scorefxn.eval_ci_2b() can compute the pairwise energy between residues for a given scorefxn. This works for the LJ, Solvation and electrostatic potentials. Also as epxected, it ignores intra-residue interactions and backbone parameters when computing with eval_ci_2b(). However, I was wondering why the Hydrogen bonded potential is also not included? Is there an easy way to include the hydrogen bond energy in the pairwise energy?

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PyRosetta - General

splitfile.py

Submitted by saladi on Fri, 2018-03-30 10:31
Category: 
Docking
Small Molecules

I'm looking at the methods of the following paper:

Elife. 2017 Sep 19;6. pii: e28909. doi: 10.7554/eLife.28909.
Computational design of environmental sensors for the potent opioid fentanyl.
Bick MJ#1, Greisen PJ#1, Morey KJ2, Antunes MS2, La D1, Sankaran B3, Reymond L4,5, Johnsson K4,5, Medford JI2, Baker D1,6.

and trying to follow along (to eventually adapt it for my own work).

I've hit a snag at one of the commands:

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Rosetta 3 - Applications

Clustering issue

Submitted by Loki01 on Thu, 2018-03-29 10:16
Category: 
Scoring

Dear all,

 

I am using Calibur to create my clusters. I dont understand the output.

It shows there are two large clusters and lists the centroid. Then it goes on showing the content on the largest cluster, but the not the second cluster. Then it lists another 2 clusters. However, why is the second cluster missing?

Also, the total of decoys doesnt add up. It should be 1000 but its much less.

I am a bit confused as to how many clusters do I have in total and where there are listed.

 

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Rosetta 3 - Applications

cleanATOM() for non-ideal amino acids

Submitted by ac.research on Thu, 2018-03-29 07:50
Category: 
PyRosetta

Hello People,

 

I am trying to clean this protein 3HZ7.pdb using pyrosetta.toolbox.cleaning.cleanATOM('3HZ7.pdb') in order to use it within PyRosetta.

The protein has MSE (Selenomethionine?) instead of MET at different parts of the sequence, therefore when applying cleanATOM() it just deletes these amino acids and I end up with a broken backbone (attached figure).

 

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PyRosetta - General

hbnet

Submitted by mintseris on Mon, 2018-03-19 09:02
Category: 
Scoring

Hi,

I'm trying to use hbnet in my design score function but get an error.  Is this a known issue or am I doing something wrong? Here's a stripped down script:

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Rosetta 3 - General

Secondary Structure Relax

Submitted by ac.research on Sat, 2018-03-17 10:50
Category: 
Design

Hello everyone,

I have generated a protein, and as you can see it seems to have almost a good backbone structure (the helices and the sheets are clearly visible but not quite there). Attached are two photos, Figure 1 is what I have generated, Figure 2 is the original crystal structure.

Is there a way to relax the structure as to emphasise for the secondary structures. In other words, push the structure to form secondary structures? or complete the hydrogen bonds for secondary structures?

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Rosetta 3 - General

PyRosetta compiled with GLIBC 2.12

Submitted by santanajuan on Tue, 2018-03-13 15:02
Category: 
Compilation
PyRosetta

Hello,

We are trying to install PyRosetta on CentOS 6.  The current compilation of PyRosetta (PyRosetta4.Release.python27.linux.release-171.tar.bz2) requires GLIBC_2.14.

However, our system's GLIBC version is 2.12 and the compilation of PyRosetta stop with the error

                          ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cm/shared/apps/pyrosetta/python/2.7/4.171/lib/python2.7/site-packages/pyrosetta-2018.9+release.333d996-py2.7-linux-x86_64.egg/pyrosetta/rosetta.so)

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PyRosetta - Build/Install

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