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AbinitioRelax Disulfide Bonds are not being retained

Hi All,

I am using Rosetta AbinitioRelax, and for the most part, it seems to be going alright. However, when I introduce a disulfide bond, the application executesas normal, yet does *not* seem to retain the disulfide bond. I have seen this complication elsewhere on this forum, but there doesn't seem to be any correct advice on how to solve the problem.

My flags are:
-database $DATABASE
-in:file:fasta sequence.fasta
-in:file:frag3 fragments.3
-in:file:frag9 fragments.9
-in:fix_disulf disulfide.ss
-in:file:fullatom
-out:nstruct 10000
-out:file:silent structures_silent.out

Post Situation: 

Rosetta can't handle symmetric fold and dock for >10-subunit protein?

I am trying to fold and dock a 12-subunit protein which adopts a D6 symmetry. I made the symmetric definition file by
running "make_symmdef_file_denovo.py -symm_type dn -nsub 12". Then I run the "minirosetta.linuxgccrelease" application to do the ab initio folding and docking, and it gave me the following error

-----
ERROR: [ERROR] VRT VRT00010 not attached to a subunit
ERROR:: Exit from: src/core/conformation/symmetry/SymmData.cc line: 1099
-----

Post Situation: 

libmini.dylib

Hi there,

I am a new user of PyRosetta. I downloaded PyRosetta.MacOSX.Lion-r44597.64Bit on my mac.
I can import rosetta module without any problem and use some of the functions in it. But when I use myfunction = create_score_function('standard'). I got segment fault 11 and the error message is: Python quit unexpectedly while using the libmini.dylib plug-in.

Is there any idea how to solve this problem? Thanks!

Post Situation: 

Using FastSAXS Scoring Protocol

Hello,

I apologize for being so persistent when it comes to posting in this forum but I came across another issue I cannot resolve myself.

After reaching the final stages of my structure calculation I would like to include SAXS scoring. Normal SAXS scoring using the "saxs_score X" flag in a scoring file works but takes ages (up to 6 h compared to 12 min without SAXS) to finish one structure. Therefore I would like to try the latest and as far as I am aware from the literature also best SAXS scoring; termed "FastSAXS" in Rosetta3.3.

Post Situation: 

problem with glibc when installing pyrosetta on RedHat Enterprise cluster

Hi everybody.
I was "installing" PyRosetta on a linux cluster, i got a tough problem when trying to run "from rosetta import *":
*****************************************
Traceback (most recent call last):
File "", line 1, in
File "rosetta/__init__.py", line 14, in
import utility, core
File "rosetta/utility/__init__.py", line 1, in
from _rosetta_utility_000 import *
ImportError: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by rosetta/utility/_rosetta_utility_000.so)
*****************************************

Post Situation: 

[SOLVED] swamped memory

Hi Rosetta users,
I have experienced some memory problems when loading a minirosetta threading application. I've asked for 10000 structures per run and launch several process in a cluster.
Rosetta consumes the memory slowly util starts using swap. At this point, the system cpu load gets higher and higher so that almost no more structures are built.
The amount of memory is 2GB per cpu. Is this Rosetta behavior normal? or do I miss some expert Rosetta keyword?

Post Situation: 

Problem With Rosetta3.3 Comparative/Loop Modeling And Constraints

Hello,

I downloaded last Friday's - 9/9/11 - Rosetta3.3 version (curious to try the "fastsaxs" scoring) but there seems to be a problem in Rosetta3.3 when handling constraints.

Running a script like the one posted elsewhere causes an exception under minirosetta 3.3, while 3.2 is able to run the very same script without problems. Here is what the message reads:


protocols.moves.MonteCarlo: QuickCCD trials= 450; accepts= 0.1111; energy_drop/trial= -7.19030

Post Situation: 

Refinement using low-resolution electron density

Dear PyRosetta (and Rosetta) developers and Users
I was wondering if there was a way within Pyrosetta to refine a PDB structure using a low resolution X-Ray or cryoEM map. Did you develop something like this within your framework? I have seen that this is possible within Rosetta, but the whole point of using PyRosetta (for me) is to have an easy to use system that can interface with other Python utilities.

Post Situation: 

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