You are here

Home

Solved

The problem has been solved

Cannot get a negative score after relax

Submitted by kxiao on Tue, 2014-01-28 22:28

Dear rosetta_users,
I am trying to relax a subunit of a actin filament(PDB ID: 3g37, chain O).
I have deleted all the modification and ligands, generated side-chains atoms by using MaxSprout, and add missing atoms by DeepView. Then I tried to use the relax function of rosetta before next step, with constraint. However, the total score of the structure is ~1200, which seems unreasonable. I also got OPT-H WARNING about chi angle, so I wonder if the high score is related with these warnings. What can I do to get a negative, at least much lower score of the structure?

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

do mpi apps share memory?

Submitted by fred on Thu, 2014-01-23 11:49

Hi there,
When using Rosetta's non-mpi applications I had a limit to read silent files of 16GB at most, which is the ram memory of one node. Do the Rosetta's mpi applications also share memory? I mean, would be possible to read silents files bigger than the memory of one node?
Thanks in advance.

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

Abinito for Multimers

Submitted by Prasanth Kumar on Wed, 2014-01-22 17:45

Dear friends,

I am new to rosetta, so can someone help me to figure out how to do ab-initio for a subunit in a multimeric protein.

I am interested in doing ab-initio for one subunit whose crystal structure is not known and the crystal structures of other non-covalently interacting subunits are completely known. It is experimentally known that the subunit whose crystal structure is not known is predominantly helix and also the approximate position of the helix is also known.

Please help me!!!

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

rosetta's keyword list

Submitted by fred on Tue, 2014-01-21 06:03

Hi there,
Is there a Rosetta keyword list somewhere? There are some keywords that cannot be found issuing the command option "-help".
To be more specific, there aren't neither the keywords constant_seed nor jran in minirosetta -help. I also could not found these keywords in the online manual. Thanks in advance.

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

is_aromatic function

Submitted by jadolfbr on Mon, 2013-12-02 19:31

Hey All,

This is probably something stupid, but I'm trying to use the is_aromatic function of Residue via python and c++ and everything returns false in a few different poses where aromatics are present.

for i in range(1, p.total_residue()+1):
print p.residue(i).name3() +" "+repr(p.residue(i).is_surface())

I have checked the params files of some aromatic side chains to make sure it is listed in the properties line, and that seems to be fine.

Am I missing some nessessary call to another function?

Post Situation: 
Solved
Forums: 
PyRosetta - General

Score - Strange message

Submitted by Ashafix on Wed, 2013-11-20 15:23

When I was trying to rescore and combine a list of PDB files which were created by loop modeling with the score application I get the following message:
hey is this the right thing to be doing???

It seems that the silent file is OK, as well as the score file. Does this message mean anything?
Google wasn't very helpful, only a BOINC/Rosetta@home user with the same message.

The command I was using:

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

change dihedral angles of any residue

Submitted by bharat_46010 on Fri, 2013-11-15 00:30

Hi,

I am interested in changing the psi-psi angles of two residues in a turn. When I use set_phi/set_psi command to change the angles, it completely disrupts the structure. Is there any way to only change the dihedral of those two residues alone without changing/disrupting the structure. I tried the same thing in Pymol, but there also I get the same disrupted structure. Can anybody suggest some other tool ??

Is it wrong to change dihedral angles of certain region and freeze the other regions of protein ??

Pls reply..............

=========
BHARAT

Post Situation: 
Solved
Forums: 
PyRosetta - General

Documentation of ``mysterious'' protocols

Submitted by ñ on Wed, 2013-10-30 08:19

Hello,

I've been using PyRosetta's pre-packed protocols like ClassicRelax, FastRelax and LoopMover_Refine_CCD thoroughly, but I've been unable to find documentation of these. I would like to know which steps are taken by these protocols in order to complete their tasks; if such information is available, could someone link me to it?

In Workshop #5: PyRosetta Refinement, it is pointed that ClassicRelax is the standard Rosetta refinement protocol, similar to this one (http://www.sciencemag.org/content/309/5742/1868.long); finding a paper describing the other protocols would be very nice.

Post Situation: 
Solved
Forums: 
PyRosetta - General

Pages

Subscribe to RSS - Solved