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missing residues while Rosie Modeling

Submitted by jguan on Mon, 2014-08-11 06:56
Category: 
Structure prediction

Hi all,
I submitted one job for anitbody variable domain structure prediction through Rosie recently. Rosie generated the pdb files. However, when I checked it through Chimera, we found the light chian C-terminal lost two residues (-RA). I double checked my submiting sequence, it was fine. Does anybody meet the similar issue? How could that happen and how to deal with it?
Thanks,
Jian

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ROSIE - General

mutate_residue not working

Submitted by lanselibai on Mon, 2014-08-11 03:55
Category: 
Design

Dear Sir or Madam,
Can I ask how to properly use the command of
mutate_residue(pose, 49, 'E') ?

It seems to be quite straightforward as pose name, residue number and amino acids are included into the parenthesis. However, I have been told
"MemoryError" (attached) after typing

from toolbox import mutate_residue
mutate_residue(A10, 3, 'E')

Do I need to type something else before using this command?

Basically, I want to mutate several amino acids into customised ones. Is this the best way to do?

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PyRosetta - General

how can i refine protein loop region contain nonstandard amino acid morespecifically Phosphoserine and phosphothreonine

Submitted by jai_INMAS on Thu, 2014-08-07 01:49
Category: 
Loop Modeling

Recenly i have modeled one protein pknQ, its a kinase and contains phosphoserine and phoshothrionien at their activation loop region. I have used homology modeling methods to predict the 3D structure of pknQ and further refined the loop. I have modified the serine and threonine to phosphoserine and phosphothrenine now to minimize the effect of post translation modification i want to further refine loop having nonstandard amino acid (phosphorylated serine and threionine). How can i do this not getting any idea . please help

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ROSIE - General

HBNet and RosettaScripts

Submitted by protos_heis on Tue, 2014-08-05 06:05
Category: 
Design

I recently learned about a new Rosetta module for scoring hydrogen bond networks as part of protein design called HBNet. I was interested in trying out this module but I'm not sure how to use it. Recently I compiled one of the weekly releases of Rosetta3.5 so I think we have the most up-to-date software. HBNet is a RosettaScripts module I believe but I was wondering if someone could provide a sample XML script that I could play around with if it is not too much trouble. Thank you for your assistance!

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Rosetta 3 - Applications

Adding noncanonical amino acid (PCA) to Rosetta 3

Submitted by JuliusSu on Fri, 2014-08-01 11:23
Category: 
Chemically Modified Residues

Hi everyone, I'm in the process of trying to incorporate a non-canonical amino acid into Rosetta, namely pyroglutamic acid: (or 5-oxo-L-proline)

http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=PCA

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Rosetta 3 - General

Building with "extra=graphics" on Linux?

Submitted by hansellt on Fri, 2014-08-01 06:09
Category: 
Compilation

I was trying to build Rosetta_2014.22.56873 with "extras=graphics" enabled on Debian linux 7.5

I get a number of errors related to narrowing conversions while building viewers.cc

Apparently "-Werror=narrowing" is set as a flag, and I was wondering what kind of trouble i would be getting my self in for if I just changed that flag and compiled it anyway.

I've attached a listing of the build and the errors received

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Rosetta 3 - Build/Install

Inconsistencies in full atom energy calculations

Submitted by dsim on Tue, 2014-07-29 06:02
Category: 
Scoring

Hello,

I'd like to decompose the energy in one body energy terms (for each residue) and pairwise energy terms for residue-residue interactions.
I tried to check if I could decompose these terms and sum them up to retrieve the score returned by the scoring function.
The problem is that I try 3 different ways of computing the energy, and I get 3 different numbers.
Could someone please tell me what's wrong ?

Here is my code:

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PyRosetta - General

Bug in the BuildBindings.py with Linux kernel version

Submitted by Cyril Cros on Mon, 2014-07-28 12:07
Category: 
Compilation
PyRosetta

Hi,
I think I have found a rather minor bug. It happens only with Linux. I don't know if there is a report system for this, so I am posting it on the forum.
Thanks for your work with Rosetta, it is really amazing.
Cyril

Context:
I am building pyrosetta from source, using the BuildPyRosetta.sh generated by rosetta/tools/PyRosetta.develop/DeployPyRosetta.py.

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PyRosetta - Build/Install

Docking on mpi.

Submitted by Pernille on Mon, 2014-07-28 08:40
Category: 
Docking

Hi guys

Our local cluster has recently ,finallly, helped me to get the mpi Rosetta version installed.
RosettaDock seems to be working though I get some error messages. None of which i observe on my local computer.
1st:
Created 6242 residue types
Number of residue types is greater than MAX_RESIDUE_TYPES. Rerun with -override_rsd_type_limit. Or if you have introduced a bunch of patches, consider declaring only the ones you want to use at the top of your app (with the options) with the command option[ chemical::include_patches ].push_back( ... ).

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Rosetta 3 - Applications

Evaluating energies on non-standard rotamer set

Submitted by pachecoj on Sat, 2014-07-26 16:27
Category: 
Structure prediction

Without getting too detailed I would like to be able to compute all one-body and two-body energies for a set of chi angles that I have chosen (e.g. that are not from a rotamer library). I am evaluating for a set of angles for each chi rather than a single joint configuration, and would like to compute and store this set of energies. It seems like the way to go would be to build up a RotamerSets object on-the-fly as in:

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Rosetta 3 - General

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