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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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Rosetta 3 - Applications

the extracted pdb file

Submitted by benniu2004 on Fri, 2013-01-04 17:55

Hi,
I used the rosetta3.4_membrane_homology_modeling to build a pdb file. but when I extract them from the silent file, my target pdb didn't looks like a normal protein, even like a jumble of segments.

Did I make a mistake?

the silent file was created by this command line: ~/rosetta3.4/rosetta_source/bin/minirosetta.linuxgccrelease @flags, and the flag file was attached.

to extract the pdb file from silent file by: ~/rosetta3.4/rosetta_source/bin/extract_pdbs.linuxgccrelease @convert.flags,and the convert.flag was also attached.

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Rosetta 3 - Applications

Rosetta 3.4 on Mac OS X v 10.6.8

Submitted by aroop on Fri, 2013-01-04 06:11

Hi!

I just downloaded Rosetta 3.4 from the RosettaCommons website and am trying to compile it. However, it keeps failing with the following message (while Rosetta 3.3 compiles fine) :

Background:
Processor: 2.66 GHz Intel Core i&
Memory: 8 GB 1067 MHz DDR3
Command Line: (executed from within rosetta_source directory): ./scons.py bin mode=release

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Rosetta 3 - Build/Install

to create the template pdb file

Submitted by benniu2004 on Sat, 2012-12-29 23:04

Dear everyone.

I used the rosetta membrane homology modeling, recently, when I tried to create the template pdb file by the script createTemplate.pl, the error of "attempt to assign missing density from parent[86] as a takeoff for query[167]" occurred. it righet that the parent pdb file do have 86 residues.

my zone file is :
zone 17-29 : 1-13
zone 41-46 : 14-19
zone 80-82 : 20-22
zone 88-92 : 23-27
zone 110-167 : 29-86

the aligment file is:
>quary
SVKKLADVMVLTVFCLSVFALIGLQLFMGNLRHKCVRNFTALNGTNGSVE
ADGLVWESLDLYLSDPENYLLKNGTSDVLLCGNSSDAGTCPEGYRCLKAG

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Rosetta 3 - Applications

membrane ab initio error after montecarlo

Submitted by adva on Mon, 2012-12-24 01:43

Hello,
I'm running rosetta 3.4 membrane abinitio protocol. Right after it says the total weighted score of the monte carlo of the second stage I get this error messege:

ERROR: seqpos <= size()
ERROR:: Exit from: src/core/conformation/Conformation.hh line: 289
membrane_abinitio2.linuxgccdebug: src/utility/exit.cc:155: void utility::exit(const string&, int, const string&, int): Assertion `false' failed.

my command line is:

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