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Creating centroid patches for Proline (pro_hydroxylated_case1 and pro_hydroxylated_case2)

Submitted by skovacs on Thu, 2012-05-10 20:10

Greetings,

When trying to dock two proteins (with ligands), I obtained the following error:

can not find a residue type that matches the residue PRO_p:pro_hydroxylated_case1at position 31

ERROR: core::util::switch_to_residue_type_set fails

ERROR:: Exit from: src/core/util/SwitchResidueTypeSet.cc line: 135

When I review the log file, I see the following:

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4219 residue types

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Rosetta 3 - General

ddg_monomer conformational search...

Submitted by yperez on Wed, 2012-05-09 11:10

Hi,
I'm fairly new to using Rosetta suite, so sorry if silly questions. I'm running ddg_monomer app for a protein of about 150 aa.

A) the pdb outputs I get are all the same, there is no backbone or sidechain movement neither for wt nor for mut structures (50 for each as recommended). I intended to carry out the protocol of row 16 in Kellogg, 2011. I attached the options file, if you'd be so kind to take a look at it. What am I missing here?

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Rosetta 3 - Applications

Unpredictible amino acid replacements

Submitted by Victor on Wed, 2012-05-09 09:21

During loop modeling using loop_modeling.py from http://www.pyrosetta.org/scripts
and using my frag3 file for my protein I found that unpredictable amino acid replacements occur for my protein.
Could you please tell me why it is happened and how to avoid this situation,
as I do not want to change my amino acids during loop modeling.

Thank you,

Victor

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PyRosetta - General

fixbb program

Submitted by Lindsay on Tue, 2012-05-08 13:56

Dear ALL,
When compile the program with scons, I don't see any Makefile which says that which source files make the fixbb binary program. What should I do to see this kind of information? I want to see which files are involved with the fixbb design program. Thank you!

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Rosetta 3 - General

Problems with boost

Submitted by vasek on Mon, 2012-05-07 01:56

Short story:

I get a segmentation fault when I issue:

from rosetta import *

in function PyInt_FromLong. But I am not sure what is wrong, since PyRosetta compilation worked fine.

Long story:

The binary distribution PyRosetta.MacOSX.SnowLeopard-r48781.64Bit works on my computer with the system python 2.6.1, but I would like to compile a version for the EPDPython 2.7, which I normally use. Also, I thought of this as training for a compilation on an older Centos system, for which there is no binary distribution.

I have:
-Mac OS X 10.6.8 32bit

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PyRosetta - Build/Install

symmetric docking application rosetta3.2: the docking_local_refine flag

Submitted by doranhen on Sun, 2012-05-06 02:20

Hi,
I have 2 questions regarding the high resolution stage of the symmetric docking application in rosetta3.2:
1. What exactly are the changes performed to the structure by the docking_local_refine flag (The reason I am asking this is that I want to know which clustering radius to use on the outputs and since I don't use the perturb_rigid_body_dofs flag in this stage I don't know how to set the radius for this clustering)?

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Rosetta 3 - General

Scoring with CCP4 electron density maps constraints

Submitted by xfliu on Thu, 2012-05-03 03:30

Dear all,

I have electron densities of the interface residues in CCP4 files and I want to evaluate my docking/designed models against them. It seems that Rosetta can take the "density scores" as an individual term and add it to the total Rosetta score. I am wondering if it is possible to access these functions from PyRosetta, like those living in core.scoring.electron_density. And moreover, how to calculate the pairwise scores between specific interface residues and corresponding electron densities? Any suggestions about how it works in Rosetta are also appreciated.

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