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Score and I_sc in ROSIE symmetric_docking output

Submitted by AdoCbl on Sun, 2015-08-09 00:26
Category: 
Symmetry

If one is doing a symmetric_docking run with 6 sub_units in cyclical symmetry,
is the I_sc value the total for all 6 interfaces or just 1 of the 6 interfaces?
Is the score the total for all 6 sub_units or just 1 of the 6 sub_units?
Does the score already include the appropriate contribution from I_sc?

Also, in each docking2 run, 2 plots are made: "Interface score I_sc / RMSD" and "Score/RMSD".
Why not make both of these plots for each symmetric_docking run as well?

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ROSIE - General

How to change your ROSIE username or password?

Submitted by AdoCbl on Sun, 2015-08-09 00:08
Category: 
ROSIE

Is there a way to change your ROSIE username or password?
http://rosie.rosettacommons.org/signup lets you set up a new account, and
http://rosie.rosettacommons.org/password_reset lets you change your password,
but the new password is chosen for you and sent to you in an e-mail,
which isn't the most private way to do things.

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ROSIE - General

docking2: local_docking vs docking_local_refine

Submitted by AdoCbl on Sat, 2015-08-08 23:57
Category: 
Docking

When I submit ROSIE docking2 jobs at http://rosie.rosettacommons.org/docking2/submit
there are options for local_docking and docking_local_refine docking protocols.
What is the difference between these options?
Where can I find documentation about them?

Thanks!

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ROSIE - General

PyMOL did not work from a remote machine with PyRosetta

Submitted by Jeremy1990 on Sat, 2015-08-08 21:25
Category: 
PyRosetta

Hi all,

I want to show the structures by PyMOL_mover to PyMOL in another computer,so according to the tutorial by setting pymover.link.udp_ip = #IP(where PyMOL is running) and pymover.link.udp_port = 65000,but after pymover.apply(pose),the pymol did't show anything,(if PyRosetta and PyMOL run in the same computer,it works),have anyone met this problem,thanks a lot if you can help me!

Thanks,
Jeremy

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PyRosetta - General

Error Scoring Application- Illegal attempt to score

Submitted by samuelrpita on Thu, 2015-08-06 14:45
Category: 
Scoring

Dear users
I'd tried to analyse my silent file that came from other concatenated silent files (cat *.out > 5novo.out) running the scoring application through my command line [1] but the program gave me this message:
...
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 420 in file 1IYT.pdb. Best match rsd_type: ALA_p:CtermProteinFull
core.pack.task: Packer task: initialize from command line()
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...

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Rosetta 3 - General

homology modeling with threading says length mismatch between sequence and alignment

Submitted by rqliang on Thu, 2015-08-06 11:46
Category: 
Structure prediction

HI,

I try to model my protein with two template PDBs. Later I learned that this kind of chimeric modeling hasn't been released yet. So I want to try to predict the structure of my protein with one scaffold PDB. But minirosetta says there is length mismatch. As I see there isn't length mismatch. Any comments? Thanks.

Here is what it spits out:
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...

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Rosetta 3 - Applications

autoNOE peak lists

Submitted by aep on Thu, 2015-08-06 06:15
Category: 
Constraints

Hello.
I am using autoNOE and RASREC Rosetta to try to calculate a protein structure using sparse NMR NOESY data. I am wondering if there is a way I can input a partially (manually) assigned NOE peak list into the autoNOE setup, not just a completely unassigned list. I know I can give RASREC cyana-style upl constraints, but that's not what I'm looking for. I'd like to see if I can improve the accuracy of the autoNOE sampling by giving it a few manually-determined, unambiguous noe assignments, I just don't know how to properly format that input peak list.

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Rosetta 3 - Applications

loop modeling

Submitted by bharat_46010 on Thu, 2015-08-06 01:34
Category: 
Design

Hi,

I am trying to mutate the residues of a loop using resfile but it seems that the rosetta doesn't read the resfile at all. I checked this by adding a random sentence and ran the job, which ran perfectly but with native loop sequence. Here are the options which I used for loop modeling:

flag file:

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Rosetta 3 - General

fragment building

Submitted by StevPChem on Tue, 2015-08-04 09:01
Category: 
Structure prediction

Hello
I used the Rosetta web site to generate fragments (3, 9) for the purpose of modeling a protein. The protein(template) I want to model was the template used to generate the fragments. However, when I use those fragments generated by the Rosetta server to model by template protein, I got:

core.fragments.ConstantLengthFragset: line too short skipping line

I then compare the fragment files generated by Rosetta web site to those used in a tutorial...The format is the same. Of course, the contents are different but everything else appears to be identical.

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PyRosetta - General

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