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secondary structure prediction for generation of fragment libraries

Submitted by xpzhang on Sat, 2011-06-25 00:47

I found that the "psipred" installed at three different places generated different results for one sequence (Rad59, please focus on the 40 aa at its N-terminus). Is that because their version? Which "psipred" is more reliable?

1. "Fragment Libraries" server (v2.6): http://robetta.bakerlab.org/downloads/fragments/22521/
2. the SYMPRED server (v ?): http://zeus.few.vu.nl/jobs/aeb9f401c184595c85e6ef7aaef6defe/
3. A local installed Psipred copy (v. 3.2 ?).

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Rosetta 3 - General

Floppytail modelling

Submitted by felipet on Fri, 2011-06-24 09:23

Hi,

sorry if this question is too basic, but I'm trying to use FloppyTail to model the C-terminus of a structure (the starting model was generated with robetta) and the run allways crashed.

when I run the test available (complex_readytail_final_nozn.pdb) the program works fine!

I tried many things with the pdb file, but I allways have the same problem

the options are basically the same as the test, obviusly changing the -flexible_start_resnum

the log:

Warning: no movable positions in ShearMover!
apps.public.scenarios.FloppyTail: 96 -169.666 -169.666

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Rosetta 3 - Applications

rosetta protein protein docking start up

Submitted by vk on Fri, 2011-06-24 09:01

Hi all

I just tried to install Rosetta 3.2.1 X64 bit in Redhat linux, guessing managed to install the software after initial trouble.
But do not know how to proceed to for doing docking and other usage of software. I did gone through the guide but not
clear enough for me.

Please how can I set up the environment and run either command mode or graphical interface of Rosetta for docking and other
calculations.

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Rosetta 3 - Applications

Multiple jobs for homology modeling

Submitted by justin on Fri, 2011-06-24 08:03

Dear all,

I am doing homology modeling on a ~200 amino acid protein. According to the online manual, I plan to generate 10000 decoys. However, it would take very long time (about 20 days) to finish the job using a single processor on my machine. So I tried the " -run:constant_seed -run:jran " options which is suggested in Abinitio protocol. Then I submitted multiple jobs with different "jran" seeds.
Does this work? If not, please give some suggestions!

Thanks a lot!
-Justin

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Rosetta 3 - General

Modeling of side-chains onto membrane ab initio cluster?

Submitted by akfried on Thu, 2011-06-23 04:03

Hi all,

I am running a big membrane ab initio calculation and clustering right now. So far everything ran well, and clustering gave me good results.

Now I want to remodel the best cluster into a full structure with amino acid side chains and so on. So I'm searching for an application in Rosetta, that can generate a full structure out of the low-resolution centroid models? As far as I know the original ab initio application switches between centroid modeling and refinement, so it should be possible to complete this task.

thanks a lot,
akfried

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Rosetta 3 - Applications

Ligand docking and protein design of an internal pocket in a protein with a cofactor

Submitted by oerbilgin on Mon, 2011-06-20 13:55

Hi, I am a brand new user of Rosetta... I want to model in different substrates in a transporter, and see how the substrates affect the overall protein structure. The problem is, the binding pocket I am trying to look at is pretty much in the center of the protein, so one question is: how can I define a region of the protein where I want my ligand to dock? A confounding variable is that my protein also has a cofactor covalently bound to a residue side chain. A colleague in my lab tried to help me, but we got stuck with this covalently bound cofactor issue.

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Rosetta 3 - Applications

Problem running Pyrosetta on RedHat/CentOS 5

Submitted by jadolfbr on Fri, 2011-06-17 10:06

Hi,

I'm trying to run PyRosetta on the lab's cluster:
CentOS release 5.2 (Final)
Linux version 2.6.18-92.el5 (mockbuild@builder10.centos.org) (gcc version 4.1.2 20071124 (Red Hat 4.1.2-42))
The architecture is x86_64.

I get this error when trying to import libraries for both PyRosetta Scientific Linux, and Ubuntu (Both 64bit distributions) (Version 2

Python 2.6.4 (r264:75706, Dec 10 2009, 10:49:23)
Type "copyright", "credits" or "license" for more information.

IPython 0.10 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.

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PyRosetta - Build/Install

cluster error

Submitted by sudhar on Fri, 2011-06-17 05:58

Hi all,

I tried clustering decoy pdbs from a docking run using the following command

--------------
/opt/rosetta/rosetta_source/bin/cluster.linuxgccrelease -database /opt/rosetta/rosetta_database -in:file:l ./list-of-pdbs.txt -nooutput > cluster.log3
-------------------

It seems to read the files. Below is the very end of the log file

.................
.
.
.
protocols.jobdist.main: Starting complexppk_moveddecoy_56890_0001 ...
core.conformation.Conformation: Found disulfide between residues 23 93
core.conformation.Conformation: Found disulfide between residues 135 209

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Rosetta 3 - Applications

Failure appending a residue

Submitted by rfschleif on Thu, 2011-06-16 10:53

On my system, the following produces memory errors 3/5 of the time at the third or fourth insertion step, segmentation faults 1/5, and finishes without problems 1/5. Deleting and inserting one residue always works, but the scripts become increasingly unreliable with increasing numbers of residues deleted and inserted. If this problem is not due to a correctable mistake on my part, could someone please suggest how I might dock two domains of a protein without interference from their interdomain linker, and then restore the linker (presumably by building a loop).

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