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[SOLVED]core.io.silent: [ WARNING ] ...

Submitted by fred on Wed, 2011-10-05 07:38

Hi List,
When clustering, I've got thousands of the following warning message:
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue ...
core.io.silent: [ WARNING ] (in residue 287 natoms_pose=7atm_seqpos 287 natoms_struct=11)
core.io.silentKilled

Before clustering, I have gathered several silent files using the full atom mode with the option "silent_struct_type binary". Is there something to do with the structure type?

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Rosetta 3 - Applications

Information about “membrane_highres_Menv_smooth.wts”

Submitted by Groros on Sun, 2011-10-02 03:59

Hi there,
I would like to use the weights membrane_highres_Menv_smooth.wts as it seems to be suitable for membrane proteins. Unfortunately I can’t find any further information, could anyone help me out? A paper or any other reference would be perfect.
Many thanks

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Rosetta 3 - General

input_pdb

Submitted by evo_umich on Sat, 2011-10-01 14:20

Hi there,

I got this error when I ran pyrosetta. Any ideas? Thanks in advance!

>>> pose = Pose("test_in_short.pdb")
Traceback (most recent call last):
File "", line 1, in
Boost.Python.ArgumentError: Python argument types in
Pose.__init__(Pose, str)
did not match C++ signature:
__init__(_object*, core::pose::Pose src, unsigned long residue_begin, unsigned long residue_end)
__init__(_object*, core::pose::Pose src)
__init__(_object*)

I downloaded 3ihw and parse all lines with ATOM as one of the tutorial script taught.
My pdb file is like:

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PyRosetta - General

How to deal with Cu-as a ligand or as part of the receptor?

Submitted by hanypao on Fri, 2011-09-30 18:50

Nowadays,I try to model a Tyrosine,pdb name is 2y9w,there are two Cu exists int the protein. I checked the database and found that there's no cu atom so there's also no cu params file. So i trid to make a Cu params file manually, and add Cu atom in the database,but i don't understand (NAME ATOM LJ_RADIUS LJ_WDEPTH LK_DGFREE LK_LAMBDA LK_VOLUME)in the file "rosetta-3.2/rosetta_database/chemical/atom_type_sets/fa_standard/atom_properties.txt".what the data should i add for cu and what other files should i change. Besides,what should i deal with Cu,as a ligand or as a part of receptor?

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Rosetta 3 - General

loop modelling error on Rosetta3.2 or Rosetta3.3

Submitted by exchhattu on Thu, 2011-09-29 03:58

I am trying to remodel the loop giving low-resolution electron density map. I have tried Rosetta3.2 and 3.3 however the job could not complete when I run in mpi mode. Could you have any solution for this?

The log of error is like this. It is due to mpi.

output filename: .//outdir_2/S_0003.pdb
ERROR: Unable to open file: .//outdir_2/S_0003.pdb
ERROR:: Exit from src/protocols/jobdist/JobDistributors.cc line:727

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Rosetta 3 - General

AbinitioRelax Disulfide Bonds are not being retained

Submitted by brspurri on Wed, 2011-09-28 13:55

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

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Rosetta 3 - Applications

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

Submitted by myang on Mon, 2011-09-26 11:52

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
-----

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Rosetta 3 - General

libmini.dylib

Submitted by evo_umich on Fri, 2011-09-23 14:08

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!

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PyRosetta - General

Using FastSAXS Scoring Protocol

Submitted by jurkm on Tue, 2011-09-20 07:40

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.

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