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Is a personal PC feasible to run PyRosetta?

Submitted by lanselibai on Wed, 2014-08-13 07:49
Category: 
PyRosetta

Dear Sir or Madam,
Recently I encountered some problems (e.g. Runtime error, memory error) when running PyRosetta. I am not sure whether it is due to my old PC or my incorrect code. Can I ask do you think it is feasible to install

PyRosetta.Windows.64Bit.monolith.mode=release.branch=release-r10.exe

on a PC of

AMD Athlon(tm) II P360 Dual-Core Processor 2.30 GHz
4.00 GB
64-bit OS
Win 7 Ultimate, Service Pack 1
?

Or do you run your PyRosetta work on a cluster?

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PyRosetta - Build/Install

Calculating sasa per atom and atomid_map

Submitted by ioannis.f on Wed, 2014-08-13 05:26
Category: 
PyRosetta

Hi,

I am trying to calculate the sasa for each atom but I cannot get the arguments correct for rosetta.core.scoring.calc_per_atom_sasa.

I guess for "utility::vector1< Real > & rsd_sasa" I can use rosetta.utility.vector1_Real().

However, I have trouble with "id::AtomID_Map< Real > & atom_sasa". I tried rosetta.core.id.AtomID_Map_AtomID() but it doesn't match the C++ signature.

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PyRosetta - General

task_pack.restrict_to_repacking() not working

Submitted by lanselibai on Mon, 2014-08-11 08:06
Category: 
Design

Dear Sir or Madam,
I am learning the "Monte Carlo Side-Chain Packing" in Workshop6.

After successfully typing

task_pack = standard_packer_task(pose),

I was trying to use

task_pack.restrict_to_repacking() .

However, I was told "MemoryError" (attached). Can someone tell me what is the reason? Thank you very much.

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PyRosetta - General

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

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

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