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'DockingProtocol' object has no attribute 'setup_foldtree'

Submitted by karelk on Wed, 2011-05-04 06:24

Hi around, sorry for disturbing with my problem that I haven't found posted or solved and if it has been solved I didn't find it. I recently downloaded PyRosetta and would like to use it for docking. The easiest, I thought, is to take an example script that comes with PyRosetta - docking.py, taking the test_dock.pdb that also comes with PyRsoetta and run it to get an idea about computational time. But it doesn't work by writing:
=========
docking.py in ()
15 print "setting up docking fold tree"

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PyRosetta - Scripts

Problem readin .ccp4 map file

Submitted by jljbbc on Tue, 2011-05-03 11:29

Hi all,
I have bin trying to run the electron_density/molecular_replacement demo at step 4 run_rosetta_mr_nogap.sh and I get the following error. There is nothing wrong with the ccp4 map file (opens fine in other programs)but it appears to be looking for a MRC format map. How do I get the program to accept the ccp4 map?

core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map MR.1_2mFo-DFc.ccp4. Not loading map.

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Rosetta 3 - Applications

Version of VALL Database and Corresponding Constraint Coordinate File for Fragment Generation

Submitted by jurkm on Mon, 2011-05-02 03:00

Dear all,

I realized that the latest vall database that comes with Rosetta 3.2 is version 2006-05-05. Unfortunately, there is no corresponding constraint coordinate file ("vall_cst_coord.dat.") for that database. Both database files are only available for the 2001-02-02 version. Is there a way to get the constraint coordinate file also for vall 2006-05-05?
The 2001 version contains only one-third of entries in comparison to the 2006 version.

I want to use this for fragment picking using also my experimental NMR data (can't rely on Robetta).

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Rosetta 3 - General

Problem with the -dock_ppk flag

Submitted by lzx32 on Sat, 2011-04-30 00:21

Hey everyone,

I have been running protein docking with two monomeric proteins by using Rosetta3.2. Everything seemed to be fine with the docking runs except when I added the -dock_ppk line into the flags file.

Instead of having the -dock_ppk line in the flags file, I also tried to prepack the proteins by using the command line:

/usr/local/rosetta3.2/rosetta_source/bin/docking_protocol.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ -s input1.pdb -dock_ppk

It did not work either. Here is the last portion of the log file:

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Rosetta 3 - General

Problem with symmetric docking

Submitted by saxen on Fri, 2011-04-29 15:15

Hello everyone,
I'm trying to refine a homotrimer by using symmetric docking in Rosetta 3.2.1. I built the symmetry definition file and ran the following command:

~/rosetta_bin/docking_protocol.linuxgccdebug -database ../rosetta_database -in:file:s INPUT.pdb -in:file:fullatom -ex1 -ex2 -symmetry:symmetry_definition symdef.txt -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8 -nstruct 1 -out:file:fullatom

Which yielded the following output

core.init: Mini-Rosetta version exported from unknown

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Rosetta 3 - Applications

Symmetric docking - tetramer of trimers

Submitted by SenyorDrew on Fri, 2011-04-29 08:26

I'd like to model a tetramer of trimers. In this situation I'm trying to ensure that all monomers end up on the same X-Y plane. Does anyone have any idea what my symmetry definition file should look like for this? Here's how I initially tried to do it, but I'm not getting reasonable looking structures:

------------------------------
symmetry_name sweeden_rules
subunits 12
recenter
number_of_interfaces 10

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Rosetta 3 - General

test/run.py errors

Submitted by kingljy on Fri, 2011-04-29 06:57

When I input test/run.py on /resetta_source in rhel5.6 or 6,I all got the follow erros,
[root@localhost rosetta_source]# test/run.py -database /rosetta/rosetta_database
Identifying platform...

Platform found: debug/linux/2.6/64/x86/gcc/
Paths: cd build/test/debug/linux/2.6/64/x86/gcc/ && command line: ./protocols.test --database atabase
bash: ./protocols.test: No such file or directory
Paths: cd build/test/debug/linux/2.6/64/x86/gcc/ && command line: ./core.test --database atabase
bash: ./core.test: No such file or directory

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Rosetta 3 - Build/Install

Using Rosetta Docking for nucleic acids

Submitted by Adrien Guilhot on Thu, 2011-04-28 06:16

Hi,

I tried to use RosettaDock with protein-nucleic acid chains. But I have a problem. Rosetta doesn't seem to recognise nucleic acids with the parameters I used. Here is the error message:


ERROR: unrecognized aa U
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 534

The version of RosettaDock I compiled (3.2.1) worked with the protein-protein complexes I tried.

I suppose there is a command to specify nucleic acids or a specific database to use. Can anybody please tell me how to use RosettaDock for protein-nucleic acid chains?

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