The problem has been solved
Hello,
is HBNetStapleInterface avaliable in the current version of Rosetta?
In 2016_15 build i get:
Error: ERROR: Exception caught by rosetta_scripts application:HBNetStapleInterface is not known to the MoverFactory. Was it registered via a MoverRegistrator in one of the init.cc files (devel/init.cc or protocols/init.cc)?
Best wishes,
Staszek
I am having a problem when setting the packer to design residues that are non canonical in the pdb file I provide. I have an example for 2ovq where the short peptide called chain C has two phosphorylated residues (TPO at 380 and SEP at 384). When I make a resfile like this:
NATAA
start
384 C ALLAA
Hi,
I am using the 2016.28 build and have the some problems with "BridgeChainsMover" from Brian's recent method paper: DOI:10.1007/978-1-4939-3569-7_20
I get this error "ERROR: 'scorefxn' is not a valid option for BridgeChainsMover". Here is the part of script that returns an error:
<BridgeChainsMover name="connect" chain1="1" chain2="2" motif="3LX-3LA-3LX" overlap="3" scorefxn="centroid_scorefunction" />
Dear All,
I use IteratedConvergence in my Rosetta Script. Is there a convenient way to monitor the number of cycles that that passed before the convergence? Would it be possible to have this value for the individual models in the score file, together with total_score etc.?
This brings a more general question - how to monitor/debug Rosetta scripts, e.g. track energy values, behavior of filters etc.
Thank you for suggestions & best wishes,
Staszek
I've been trying to build the latest weekly release (2016.20), and after starting scons using:
external/scons-local/scons.py -j3 mode=release bin
from the source directory, everything will be fine for around 2h, but then I get this error:
/usr/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.2/64/x86/gcc/4.7/default/libObjexxFCL.so] Error 1
scons: building terminated because of errors.
Hello, everyone!
I have some problems while compiling rosetta_src_2016.20.58704 source code both in my desktop and cluster.
Compilers: gcc 6.1.1 & gcc 4.9.3
Compiling with make:
./make_project.py all
cd build_release
cmake ./
make -j 8
I just seperately modeled two halves of an IgG1 Fc as two seperate pdb's and I need to combine them into one. How would I be able to do that? Or just in general how would I be able to combine two pdb's into one?
Hi Rosetta users,
I was trying to generate fragment files for a short peptide (9-AA) for use in abinito FlexPepDock. I checked out the demo, but found it quite difficult to follow using make_fragments.pl. I learned from the forum that the perl script is a bit outdated and we should use either the Robetta server or the new fragment picker application. However, Robetta doesn't seem to accept very short sequences. Could anyone advise me how to use the new fragment picker application to generate fragments for short peptides. Thanks in advance!
Hello,
Multiple input structures are provided as a list (in:file:l) or in a single silent file (in:file:silent).
Is there an easy way to provide also symmetry definition files for the individual structures? (symmetry:symmetry_definition)
Thanks you for suggestions!
Best wishes,
Staszek
Hi All,
I have a design protocol implemented in PyRosetta that has a very large memory footprint ~ 4Gb. I ran a python memory profiler on the design script and discovered that the sharp memory consumption increase occurs upon the initialization of PackRotamerMover (I presume this is where the rotamer library is instantiated). I have taken the following measures to reduce the memory consumption with no success: