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Using FastSAXS Scoring Protocol

Submitted by jurkm on Tue, 2011-09-20 07:40

Hello,

I apologize for being so persistent when it comes to posting in this forum but I came across another issue I cannot resolve myself.

After reaching the final stages of my structure calculation I would like to include SAXS scoring. Normal SAXS scoring using the "saxs_score X" flag in a scoring file works but takes ages (up to 6 h compared to 12 min without SAXS) to finish one structure. Therefore I would like to try the latest and as far as I am aware from the literature also best SAXS scoring; termed "FastSAXS" in Rosetta3.3.

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Rosetta 3 - General

problem with glibc when installing pyrosetta on RedHat Enterprise cluster

Submitted by skipper on Fri, 2011-09-16 11:15

Hi everybody.
I was "installing" PyRosetta on a linux cluster, i got a tough problem when trying to run "from rosetta import *":
*****************************************
Traceback (most recent call last):
File "", line 1, in
File "rosetta/__init__.py", line 14, in
import utility, core
File "rosetta/utility/__init__.py", line 1, in
from _rosetta_utility_000 import *
ImportError: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by rosetta/utility/_rosetta_utility_000.so)
*****************************************

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PyRosetta - Build/Install

[SOLVED] swamped memory

Submitted by fred on Fri, 2011-09-16 08:19

Hi Rosetta users,
I have experienced some memory problems when loading a minirosetta threading application. I've asked for 10000 structures per run and launch several process in a cluster.
Rosetta consumes the memory slowly util starts using swap. At this point, the system cpu load gets higher and higher so that almost no more structures are built.
The amount of memory is 2GB per cpu. Is this Rosetta behavior normal? or do I miss some expert Rosetta keyword?

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Rosetta 3 - Applications

Problem With Rosetta3.3 Comparative/Loop Modeling And Constraints

Submitted by jurkm on Mon, 2011-09-12 01:01

Hello,

I downloaded last Friday's - 9/9/11 - Rosetta3.3 version (curious to try the "fastsaxs" scoring) but there seems to be a problem in Rosetta3.3 when handling constraints.

Running a script like the one posted elsewhere causes an exception under minirosetta 3.3, while 3.2 is able to run the very same script without problems. Here is what the message reads:


protocols.moves.MonteCarlo: QuickCCD trials= 450; accepts= 0.1111; energy_drop/trial= -7.19030

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Rosetta 3 - General

Refinement using low-resolution electron density

Submitted by astrofunk12 on Sun, 2011-09-11 05:06

Dear PyRosetta (and Rosetta) developers and Users
I was wondering if there was a way within Pyrosetta to refine a PDB structure using a low resolution X-Ray or cryoEM map. Did you develop something like this within your framework? I have seen that this is possible within Rosetta, but the whole point of using PyRosetta (for me) is to have an easy to use system that can interface with other Python utilities.

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PyRosetta - Applications

Residue not found in pose

Submitted by lzx32 on Fri, 2011-09-09 03:42

Dear developers,

I got the error message "Residue at chain X position 167 not found in pose" when I was trying to design a protein with a ligand (residue at chain X) bound inside using the enzyme design protocol.

What's the meaning of "not found in pose"? I assume this is not as the same as the error message "unrecognized residue".

Many thanks..

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Rosetta 3 - General

Error when clustering the output from a docking study

Submitted by jos on Thu, 2011-09-08 03:26

I want to cluster the output from a docking study.

However, when running the clustering it complains about my ligand and I get this error message:
----------------------------------------------------------
|ERROR: unrecognized aa lig |
|ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 534 |
----------------------------------------------------------

This is the option file that I've used:

-database /../rosetta_database
-in:file:l list.pdb
-extra_res_fa lig.params
-out:file:silent cluster.out
-run:shuffle
-run:trust_missing_coords

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Rosetta 3 - General

Connecting 2 Domains Via Non-Flexible Linker

Submitted by jurkm on Mon, 2011-09-05 06:10

Hello,

I originally posted my question regarding modeling of a multi-domain oligomer under a different thread. After getting a lot of useful answers and consulting Ingemar Andre off the list I am still facing one major problem.

The protein at hand consists of two domains A and B connected by a structured linker. Structural models for all three "parts" are available. How would one connect these to obtain a full-length model?

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Rosetta 3 - General

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