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Error in Building Environment Options

Submitted by anamika on Wed, 2013-05-01 02:12

I have done the building part in installation by typing

scons bin
scons bin mode=release

which says "scons: done building targets"

Now next step is Additional Build Environment Options for which i get

scons bin my_pilot_apps

**scons: building terminated because of errors**

Could you please tell me what is the next step to be followed after building. how to make File target `my_pilot_apps'?

Please help!

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Rosetta 3 - Build/Install

how to keep modeling ignored ERROR?

Submitted by eunwook on Sat, 2013-04-27 05:44

Hi, I was doing ab initio with homology.pdb.

During modeling, there is a small problem but, I want to ignore small error and keep modeling.

>>
Scores Weight Raw Score Wghtd.Score
------------------------------------------------------------
coordinate_constraint 0.010 549399852.990 5493998.530
---------------------------------------------------
Total weighted score: 5493998.500

protocols.idealize.IdealizeMover: (1) RMS between original pose and idealised pose: 72.2241 CA RMSD, 72.8871 All-Atom RMSD,

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Rosetta 3 - General

Problems when running Rosetta VIP with cofactors

Submitted by Basantab on Fri, 2013-04-26 13:31

Dear Rosetta users,

I'm trying to run Rosetta VIP on a heme protein. I started by relaxing the structure according to the protocol in the "relax_around_chemically_bound_ligand" demo. My chemically bound ligand would be the heme group, to a histidine. For this, I created *.params files for the heme group and the covalently bound histidine, and created a contraints file according to the protocol. The relaxation seemed to work fine (log.txt available), as Rosetta was able to make the connection between heme and his and apply the constraints.

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Rosetta 3 - Applications

Which rosetta for antibody modelling?

Submitted by oppopomoz on Wed, 2013-04-24 09:10

Hello everyone,

I would like to use the rosetta module for antibody modelling locally, which rosetta version is the best one?

I am trying to install rosetta antibody modelling on my computer and I do not find the readme file clear enough, is there any more material about installation/running?

thanks in advance

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Rosetta 3 - General

A table of residue-residue pair energies for residues which interact across the docking interface missing in output

Submitted by awaring on Mon, 2013-04-22 14:47

I cannot find the table of residue-residue pair energies for residues which interact across the docking interface in any of the output of the server including the stats at the lower listing in the model pdb files.
Could someone tell me if I have missed this output or how to request this output from the server?

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ROSIE - General

Initializing DockDesignParser in PyRosetta

Submitted by LiorZ on Mon, 2013-04-22 01:56

Hi!
I'm trying to parse a RosettaScript in PyRosetta. In order to do that, I need to initialize the DockDesignParser, I do it in the following fashion:

dpp = protocols.jd2.DockDesignParser()
some_job = protocols.jd2.Job(protocols.jd2.InnerJob("job",0),0)
pose = pose_from_pdb('..')
some_mover = protocols.moves.Mover() (or some_mover = protocols.rosetta_scripts.ParsedProtocol())
dpp.generate_mover_from_pose(some_job,pose,some_mover,True,"minimizer.xml")

yields the following error:
ArgumentError: Python argument types in

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PyRosetta - General

Error when running Remodel with EnzDes constraint file

Submitted by aloshbau on Wed, 2013-04-17 22:23

Hi,
I'm trying to use Remodel with a constraint file and it is exiting with an error regarding atom type. The error does not occur if I remove the enzdes:cstfile flag.

My flags look like this:
'/netapp/home/noah/rosetta/remodel_r51420', '-database /netapp/home/noah/rosetta/database_r51404', '-run:chain B', '-s 1AUT_PAR1_renum_ppk_0001.pdb', '-remodel:blueprint blueprint_1', '-ex1', '-ex2', '-use_input_sc', '-nstruct 1', '-enzdes:cstfile constraint_1'

constraint_1 looks like this:
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 1 is_backbone

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Rosetta 3 - Applications

How to prevent rotamers from being pruned from the interaction graph?

Submitted by msun on Wed, 2013-04-17 14:19

Hi everyone,

I would like to prevent the pruning/removal of any rotamer from the interaction graph. There doesn't appear to be any command line argument to do so and I've been unsuccessful at modifying the source in core:pack:interaction_graph to achieve this rather simple goal.

I would greatly appreciate any pointers to prevent Rosetta from pruning any rotamer.

Thanks,
Mark

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Rosetta 3 - General

fragment_picker error secondarysimilarity.cc line:132

Submitted by leanawen on Mon, 2013-04-15 14:33

Hi
I have tried Fragment Picker in Rosetta 3, and get the following errors:

ERROR: query_prediction -> total_residue() == query_len
ERROR: Exit form: src/protocols/frag_picker/scores/SecondarySimilarity.cc line: 132

Could you please give me some advices on how to solve the problems? Thank you very much.

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Rosetta 3 - General

Rosetta3.4 on Mac 10.6.8

Submitted by gz on Mon, 2013-04-15 10:42

I tried to install rosetta on a Mac OS 10.6.8.

I tried:
scons bin mode=release

And get following message:
scons: Reading SConscript files ...
Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git
Done. (0.5 seconds)
scons: done reading SConscript files.
scons: Building targets ...

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Rosetta 3 - Build/Install

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