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flexible backbone design (fixbb+relax)

Submitted by sdh_h on Mon, 2013-02-04 03:19

Dear all,

I want to use a two-step design procedure in which a fixed backbone design is combined with a backbone relaxation.
The two steps are supposed to be repeated alternately as long as they bring improvement in the energy.
(something like this http://www.ncbi.nlm.nih.gov/pubmed/22632833)

Which fixbb design parameters are the most important? I use -packing:ex1, -packing:ex2. But perhaps there is something else I should consider?

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Rosetta 3 - General

symmetric fixbb design with design_hpatch

Submitted by sdh_h on Sat, 2013-02-02 01:48

Dear Rosetta users,

I tried to use hpatch score in symmetric design (-score:weights design_hpatch), but I got this error (rosetta 3.3 and 3.4):

sin_cos_range ERROR: -nan is outside of [-1,+1] sin and cos value legal range

Default and soft_rep_design scores work fine. Also turning off the symmetry (designing just one monomer) makes the error disappear.

Is design_hpatch compatible with symmetric design?

Best wishes,
Staszek

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Rosetta 3 - Applications

nr.fasta

Submitted by silvia on Wed, 2013-01-23 10:08

Hi all,
I downloaded the nr database and I used the formatdb to format the database. Now I have the nr files which have been generated but I have obtained neither the nr.fasta necessary to create the filtnr by using "pfilt", nor the nrfilt files.How can I get them?

Thank you,

Silvia

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Rosetta 3 - General

Flexpep docking freezing issue at "press enter to continue"

Submitted by rlwoltz on Tue, 2013-01-22 13:31

Hi all,

I searched on the forum and couldn't find this so I hope it isn't a repeat. I'm trying to dock using flexpepdocking.linuxgcc.release. I have tried this from the command line but I have been recently have been trying to run it from a script that looks like this:

the issue is whether I run it from the command line or the script the program will not continue. this is what my screen looks like:

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Rosetta 3 - Applications

Rotamer Libraries in Pyrosetta

Submitted by protos_heis on Fri, 2013-01-18 12:02

Hello everyone. I have a quick question regarding rotamer libraries in PyRosetta. I was wondering if it is possible to read the standard Dunbrack libraries that PyRosetta uses and retrieve those rotamers or the xyz data for them in Pyrosetta. If not then it's no big deal as I could figure out a way to do it outside of PyRosetta but it would be useful if PyRosetta already has a way of doing this.

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PyRosetta - General

Fatal Python error: PyThreadState_Get: no current thread running "from rosetta import*"

Submitted by alec on Fri, 2013-01-18 10:04

I am trying to make PyRosetta run on an iMac with Mountain Lion.
I have Python 2.7 installed from the official installer in /Library/Frameworks/Python.framework/Versions/2.7/bin/python
and IPhyton installed with easy_install in /Library/Frameworks/Python.framework/Versions/2.7/bin/ipython.

Python and IPython work perfectly with other application but when I try PyRosetta something goes wrong and I obtain always the same error:

In [1]: from rosetta import*
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

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PyRosetta - Build/Install

problem with fixed_membrane option of membrane abinitio

Submitted by yescalona on Thu, 2013-01-17 15:42

Hi to all

I want the models of membrane abinitio in the same membrane center vector and membrane normal vector, so I used the option -membrane:fixed_membrane to get the center at [0,0,0] and membrane normal in the z-axis

I use this arguments to run "membraneabinitio"::

-abinitio:membrane
-in:file:fasta ../rosetta_inputs/cterm.fasta
-in:file:frag3 ../rosetta_inputs/aat000_03_05.200_v1_3
-in:file:frag9 ../rosetta_inputs/aat000_09_05.200_v1_3
-in:file:spanfile ../rosetta_inputs/cterm.span
-in:file:lipofile ../rosetta_inputs/cterm.lips4
-membrane:fixed_membrane

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Rosetta 3 - Applications

fixbb and HETATM

Submitted by doranhen on Mon, 2013-01-14 07:50

Hi,

I want to use fixbb on a pdb file that contains ions (the ions are classified as HETATM in the pdb file) in addition to the protein chain (whose atoms are classified as ATOM in the pdb file). My question is: If I use fixxb on the pdb file for repacking, will the algorithm consider the presence of the ions or will it ignore them?

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Rosetta 3 - General

Rosetta Scripts: Loop Modeling w. Selective Repacking

Submitted by aroop on Mon, 2013-01-07 08:45

Hi!

Two questions:

1) I have recently started using Rosetta Scripts and would like to know if there is a way to model a loop while optimizing chi angles of only selected residues. I remember you had previously alluded to TaskAwareMinMover - is that the route - if so how ? I am using the following XML file:

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