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Copying angles (pose.set_phi()) from a substructure with the same sequence to pose doesn't produce the exact same substructure?

Dear Rosetta Gurus,

I'm writing an extension to the Abinitio Protocol, the code I will be describing is called exactly after setup_fold() in AbrelaxApplication. Now let me describe the input and what I'm trying to do:

I use as input two poses, let's call them "model" and "prediction", both are sequencially identical.
"prediction" is the extended pose created in AbrelaxApplication::setup_fold(), "model" is a pose my class loads exterally from a pdb file of an idealized protein in a Centroid fashion.

Post Situation: 

relax constraints not minimized

To whomever this may concern,

I am trying to run relax with constraints. The constraints are read in, and I verified by hand that the values within the score output file are accurate. However, the relaxation does not seem to move the atoms to reduce the constraint score. The command I am using is relax.linuxgccrelease @inputs.inp, where inputs.inp contains the following text:

-database /gpfs/group/cdm/rosetta/3.4/rosetta_database/
-in:file:s my_file.pdb
-out:overwrite
-cst_fa_file constraints.cst
-cst_file constraints.cst
-cst_fa_weight 1.0

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Trouble building PyRosetta on Linux Mint 13 (Maya) 64-bit / Ubuntu 12.04 (Precise Pangolin)

Hi mini,

I had a little trouble building PyRosetta r46030 64-bit on Linux Mint 13 (Maya) 64-bit. This revision corresponds to PyRosetta v2.011. The problems were easy to fix but since they are currently undocumented*, I thought I would list the problems and solutions here. The main problem I had seems specific to Python 2.6 and certain Ubuntu/Mint distributions so it is no surprise that it is not in the documentation. I include all the steps I took for completeness and add some comments for those new to Linux.

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Discarding atoms for fixbb

Hi everyone,

When i use the fixbb executable under the directory of /integration/test/fixbb, Rosetta always output the following warning messages,such as:

core.io.pdb.file_data: [ WARNING ] discarding 7 atoms at position 1 in file 1l2y.pdb. Best match rsd_type: ASN_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 2 in file 1l2y.pdb. Best match rsd_type: LEU
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 3 in file 1l2y.pdb. Best match rsd_type: TYR

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AB INITIO WITH METALLOPROTEIN

Hello everyone!

I'm new in the community and I would like to know where I find information about ab initio with metalloproteins (metalloprotein abinitio relax). I just found this link in the forum that talks about docking with metal but it's not exactly what I'm looking:

http://www.rosettacommons.org/node/2259

I'm trying to generate the same results in Wang et al., 2010 (Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry, 2010, Protein Science)

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Error in core/scoring/methods/VDW_Energy.cc line: 169

When i run the set vdw for the score function: scorefxn.set_weight(vdw, 1.0) and then attempt to score a pose scorefxn(pose) i get a fatal error in the VDW_Energy. When VDW is set to 0 it goes away. The scorefxn was working fine until I added a proline to my AA sequence.
I receive the following after running scorefxn(pose)
Etable 53 46 1 8
error: Fatal Error in VDW_Energy
error: Exit from: core/scoring/methods/VDW_Energy.cc line: 169

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Ligand dock analysis

Hi all,

I am running ligandDocking application thru rosetta_scripts app. On the documentation "Rosetta Ligand Docking with Flexible XML Protocols", there is a paragraph addressing how to analyse the result.
The example can be downloaded from "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020161" in the supplement info.
I did exactly what it says on the example folder provided in the documentation but there is error relating to the residue type:

ERROR: Attempting to add a residue type with name 'CP1' but this name is already taken.

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possible error in make_fragments.pl and fix

Dear fellows,

thank you for the newly rewritten version of make_fragments.pl in Rosetta 3.4 ... it came just in time when I was struggling with the old one! In my hands/case though, there was a problem with the inclusion of secondary structure prediction from pre-calculated files. (It worked well when files were calculated on the fly with psipred / SAM installed.)

I'll try to be exact with my description of the errors in the current version:

Post Situation: 

possible error in make_fragments.pl and fix

Dear fellows,

thank you for the newly rewritten version of make_fragments.pl in Rosetta 3.4 ... it came just in time when I was struggling with the old one! In my hands/case though, there was a problem with the inclusion of secondary structure prediction from pre-calculated files. (It worked well when files were calculated on the fly with psipred / SAM installed.)

I'll try to be exact with my description of the errors in the current version:

Post Situation: 

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