Another request for help with restarts
Submitted by jasnyderjr on Tue, 2015-08-18 12:14
Category:
Docking
I have read the other forum messages related to retarting a rossettaDock run.
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Per residue scoring
Submitted by chelsell on Mon, 2015-08-17 14:43
Category:
Scoring
Hi all,
I want to be able to get score information for individual residues from my decoys. What is the easiest way to do this currently? I couldn't find a relevant option in the documentation, do I have to use RosettaScripts or something? I found some old posts on this topic, but I figured I'd ask again in case things have changed in more recent versions.
Thanks!
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Namespace PyRosetta Build for Windows?
Submitted by protos_heis on Sat, 2015-08-15 10:49
Category:
Compilation
Hello everyone. I was wondering if there was any intention to ever generate a namespace PyRosetta build for Windows? I know in the past it had been said that monolith would probably be the default in the future, but I would be interested in a namespace build for Windows because namespace seems to use much less memory than monolith.
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Abinitio protocol and X-Ray diffraction data
Submitted by allan.ferrari on Wed, 2015-08-12 12:49
Category:
Structure prediction
Hello everyone,
I was wondering if it would be possible to implement in the abinitio modeling (since de beginning) the experimental data from X-Ray crystallography like we do with experimental distances constraint. As far as I am aware there is a molecular replacement protocol but it is used only with relax protocol.
Thank you guys,
Állan.
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Multi-chain Modelling
Submitted by Sandy on Sun, 2015-08-09 14:41
Category:
Structure prediction
Hi all,
I am trying to develop a model for a protein composed of multiple identical chains (a fibril actually). I know this might be a good job for the symmetry protocol, but I do not currently have enough data to define the protein's symmetry. All I have is a few constrains and some homology modeled regions. Is there a good protocol for this situation? Broker? Abinito? I am really unsure how to handle the multiple chain aspect, or if this can be handled. On a related note, if I have a multi chain system, how should I handle the fragment files?
Thanks,
Sandy
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Can you change background color of pdb file pictures?
Submitted by AdoCbl on Sun, 2015-08-09 01:47
Category:
ROSIE
In the output of ROSIE docking2 and symmetric_docking jobs,
many pdb files are shown as cartoons with rainbow coloring
and black backgrounds. Is it possible to have an option that
would change the background color of these images to white
and perhaps render these images with a thin black outline
around the cartoon shape? I think this would use less toner
when printing and yield clearer printouts. Also, could you
include these images in the tar archive one gets via the link
"[Download all job files as tar archive]" ?
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How to improve ROSIE docking2 results?
Submitted by AdoCbl on Sun, 2015-08-09 01:22
Category:
Docking
ROSIE docking2 and symmetric_docking runs both give plots
and spreadsheets containing many columns of data.
Which spreadsheet columns best reflect the quality of a run?
Should the best runs have each plot with a narrow funnel on the left
and a rather wide flat plateau to the right?
Should there be very few points scattered above or below the plateau?
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RMSD values in docking2 and symmetric_docking runs
Submitted by AdoCbl on Sun, 2015-08-09 00:48
Category:
Docking
I am curious how ROSIE docking2 and symmetric_docking runs determine RMSD values.
For docking2 runs, are RMSD values determined between
the output\trigger_00001.dock\native.pdb file
and each output\trigger_00001.dock\proteins_*.pdb file?
If so, how is the native.pdb file made?
Is it a weighted average of all the proteins_*.pdb files
with more weight given to files with better scores or I_sc values?
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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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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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