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scorefxn.show(pose) method in python shell and IDLE

Submitted by peony on Mon, 2013-07-08 01:34

Hi,

I'm trying to write a script using IDLE. I use the method scorefxn.show(pose), however when I run module, nothing happens. When I use this method in python shell, (I mean writing single commands in standard command line with black window, not IDLE) there appears a beautiful table with energy scores. I have to add that in IDLE there is no information about any error - the only thing is that there is no table. Any ideas why?

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PyRosetta - Scripts

MakeRotLib documentation for Pyrosetta

Submitted by ltassoulas on Sat, 2013-07-06 16:15

Hey everyone, I am trying to incorporate l-ncaa 5-hydroxytryptophan into a protein and I am currently stuck on making the rotamer library for it. I have made a make rot lib options file (attached). I am wondering what the next step is. There is a tutorial for the Make_Rot_Lib protocol in c++ but I was wondering what the pyrosetta protocol equivalent was. Thanks!

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PyRosetta - General

score terms

Submitted by qlj on Wed, 2013-07-03 08:00

I want to know the meaning of each score term. For example, what does fa_atr,fa_rep,fa_sol,fa_intra_rep,fa_pair,fa_plane,fa_dun,hbond_lr_bb,hbond_sr_bb,hbond_bb_sc ,hbond_sc,dslf_ss_dst dslf_cs_ang,dslf_ss_dih,dslf_ca_dih or pro_close in score12 measures, respectively? Where I can get that information.
Thank you very much!

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Rosetta 3 - General

Do I need to uninstall rosetta before installing the MPI version?

Submitted by ritacc18 on Tue, 2013-07-02 14:24

Hi,

I want to make the Rosetta 3.4 paralleled. But I have installed the ordinary one previously.

Do I need to uninstall it and then install the MPI one? If so, is there a command to uninstall Rosetta, or I just need to delete the rosetta folder?

I know I just need to add "extras=mpi" in the command.

Thanks for your help!

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Rosetta 3 - Build/Install

printing our per-residue energies including H-bonding energies

Submitted by vijayan on Tue, 2013-07-02 08:51

Hi all

Could anyone help me out in figuring out a way for printing out per-residue energies including the "hydrogen bond energies" using Rosetta 3.4. It sounds that the per residue energies obtained at the end of the annotated PDB files doesn't includes the hydrogen bond energies, as Rosetta stores H-bonding energies only on a per-pose basis. This results in inconsistencies between the sum of per residue energy and the total energy reported by Rosetta.

Thanking in advance

Regards,
Vijayan.R

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Rosetta 3 - Applications

Discrepancy between the total pose energy and sum of per residue energies

Submitted by vijayan on Tue, 2013-07-02 07:24

Hi all

I tried summing up all the per residue energies reported by Rosetta 3.4, and figured out that the sum of the per residue energies dosent match with the total pose energy reported at the end of the annotated PDB file. Could any any explain the discrepancy or am i missing out some thing.

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Rosetta 3 - Applications

membrane modeling error

Submitted by benniu2004 on Mon, 2013-07-01 17:59

Dear everyone,

recently ,I tried to model a structure of a membrane protein.

Do the following script, I created a template.However, the result seems does not reasonable.

${mainpath}/scripts/createTemplate.pl -zonesfile domain1.zone -fastafile ${target}/t000_.fasta -parentpdb renum.pdb -outpdb domain1.pdb

for the S4 segement not match the parentpdb.

The alignment file was as this:

Q_domain1/1-289 ILVHSLFNMLIMCTILTNCVFMAQHDPPPWTKYVEYTFTAIYTFESLVKILARGFCLHAF
parent IVESSFFTKFIIYLIVLNGITMGLETSKVYTTLFNQIVITIFTIEIILRIYVHRI-----

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Rosetta 3 - Applications

Problem of installing PyRosetta on Mac Lion

Submitted by sing0621 on Mon, 2013-07-01 13:13

Hello,

I am currently a new user on both Rosetta and Python. I have a Mac and here are the information:

Mac Duo Core
OS 10.7.5
Python 2.6.2
GCC 4.0.1
Xcode installed

I was trying to install PyRosetta according to the instruction on the website. However, when I get to the step

import rosetta; rosetta.init().

I got the following error message:

ImportError: dlopen(rosetta/utility/__utility_all_at_once_.so, 2): no suitable image found. Did find:
rosetta/utility/__utility_all_at_once_.so: mach-o, but wrong architecture

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PyRosetta - Build/Install

Up to date Vall database

Submitted by JadAbbass on Sat, 2013-06-29 10:35

Dear all,

I want to know how to create an up to date vall database (contains all current PDB's structures) used for fragment_picker.
I have downloaded nr.gz from:

ftp://ftp.ncbi.nih.gov/blast/db/FASTA/

Would you please state the next steps/statements to be executed?

What about the Robetta server? which version does it use to create fragments libraries?

Thank you in advance.

Jad

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