The problem hasn't been solved
Hi everyone,
First of all thanks you for the replies to other post as that has helped me to progress on using Rosetta.
I have generated structures using enzyme design but I am struggling to understand the energy scores.
Hi Rosetta guys
I am using the Intherface analyzer (script version) for post analysis of docking results. I get these odd warning messages in the log file which I cannot seem to find information on:
Hello,
In my version of PyRosetta, which I downloaded in december 2014, the mutate_residue function doesn't mutate the sequence of the Pose...
Here is the relevant part of my code:
for j in sequence:
(...)
mutate_residue(pose,resn,j, pack_scorefxn=score_fxn)
(...)
jd.output_decoy(pose)
When I do this, pose doesn't change even though its whole sequence should be replaced.
Rosetta has some applications that can be used to setup a protocol to compute the ddG of binding upon mutation (relax, fixbb or ddg_monomer to create wt structure and mutated structure, InterfaceAnalyzer to compute binding energies, etc.) Are there references available where Rosetta is used this way? Until now I have found papers where the authors either fit their own energy function to experimental data (instead of using Rosetta's energy function), or they use other applications (molecular dynamics, for example) to relax their structures, or something else.
I get the following error that terminals the build process:
src/protocols/jd2/SingleFileBuffer.cc:148:13: error: 'sleep' was not declared in this scope
It would appear that for this system "sleep" is found in the <unistd.h> include file.
Anybody else had this problem ?
Or is this a "dead" issue since 3.4 will not be getting any more updates ?
Hi all,
I want to use the RosettaSurface algorithm and I first want to try to run surface_docking.py on the osteocalcin example given in demos (/demos/protocol_capture/2013/surface_docking/PyRosetta surface docking/).
Hello everyone,
I am trying to perform a B3protein design tests using rosettascript (rosetta demo model). I have 3 designable positions and I am interested in the functionalities of the movers:"RandomMutation" and "GreedyOptMutationMover"
Using these movers, none of my design positions have been taken into account as a designable! In the log file, there are warnings
indicating that there is no design position.
Good Afternoon,
I'm running the high-res protocol of the ddg_monomer on a 439 residue enzyme structure (following the the Kellogg paper and online docs protocols) and I'm seeing some odd score outputs.
There are three types of odd outputs in the ddg_predictions.out file:
Hello
Recently, I am trying to predict flexible tail region of protein by using Floppy tail.
First I tried to use Floppy tail with test data (4tailstestdata.pdb).
I have run Floppy tail as below command
mpiexec -np 4 FloppyTail.mpi.linuxgccrelease -in:file:s 4tailstestdata.pdb -in:file:movemap mapmover -nstruct 4
//movemap
RESIDUE 90 117 BBCHI
RESIDUE 207 233 BBCHI
RESIDUE 324 351 BBCHI
RESIDUE 441 468 BBCHI
and I got 4 pdb files those file and each model has different amino acid sequence.
Dear all
sorry for the dumb question, but how can I get the number of residues on a specific chain of a complex?
thanks in advance
felipet