Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Collecting 3.2 documentation holes
- This topic has 23 replies, 7 voices, and was last updated 12 years, 7 months ago by
Anonymous.
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January 26, 2011 at 6:39 pm #749
Anonymous
The purpose of this topic is to collect holes in the 3.2 documentation. If you post a question here (and you may), please also echo it as its own thread, and look for answers there. I will collect questions from other topics into this topic, but I won’t be answering here. Once we get our next major documentation drive going, we’ll try to get all the documentation flaws exposed here patched. Feel free to post any issues with the documentation you know about; the more specific the issue the more likely we can fix it. Thanks.
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January 26, 2011 at 8:50 pm #4864
Anonymous
Executive summary: How does one generate custom fragment libaries from rosetta-annotated sequences / fastas?
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January 27, 2011 at 6:59 pm #4883
Anonymous
There is no documentation for the residue_pair_jump_cst file type (metalloprotein_abrelax integration test, read by protocols/jumping/ResiduePairJumpSetup)
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January 27, 2011 at 11:13 pm #4886
Anonymous
There’s a buglet in the install docs on http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/scons.html .
The Scons download link has the period inside the anchor tag, which results in the URL being a 404.
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January 28, 2011 at 3:13 pm #4888
Anonymous
There’s actually three instances of period inside anchor tag on that page.
First paragraph:
http://www.scons.org/doc/1.1.0/HTML/scons-user/book1.html.Second paragraph:
http://www.scons.org/download.php.
http://www.scons.org/doc/HTML/scons-man.html.
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February 6, 2011 at 2:01 pm #4962
Anonymous
The 3.2 relax and score documentation do not mention anything about NMR or NOESY. However, the 3.2 version of “relax -help” and “score_jd2 -help” suggests a wide array of NMR-related options. It would be really great to know more about the NMR-related possibilities. I am an NMR guy in the first place… so if there is more NMR functionality in 3.2, I would really love to know about it.
attachment is a partial output from “relax -help”
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February 9, 2011 at 7:21 pm #5000
Anonymous
A) check FloppyTail documentation vs. “publication mode”
ensure that AbinitioRelax does not default to looking for Oliver’s directory for the minirosetta_database
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February 14, 2011 at 3:02 pm #5017
Anonymous
A) How does one perform “partial abinitio” where some of the structure is known, and left fixed?
ANY documentation on Rosetta plus NMR. How does Rosetta use chemical shifts (is that CSRosetta?) What about NOEs and RDCs?
C) How do you get MPI Abinitio/relax? AbinitioRelax.cc doens’t do it. minirosetta.cc with the broker option appears to – but what flags does it use?
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March 1, 2011 at 9:08 pm #5102
Anonymous
Score application documentation still refers to 3.1 score.cc, not 3.2 score_jd2.cc
There is no RNA mode whatsoever in 3.2 (!!!!)
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March 8, 2011 at 7:16 pm #5135
Anonymous
There is still no way to do abinitio MPI in 3.2 – technically the “broker mode” of minirosetta.cc can do it, but there is no documentation for it.
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March 9, 2011 at 3:19 pm #5141
Anonymous
Docking partners flag uses underscore to separate groups
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March 9, 2011 at 9:01 pm #5144
Anonymous
https://www.rosettacommons.org/node/2332
AbinitioRelax A) produces silent files by default, and
suggests nonexisting executeables to convert them to PDB
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March 9, 2011 at 10:42 pm #5147
http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_fixbb.html
In the box listing flags for rotamers, I found one flag called preserve_input_cb which is supposed to keep unidealized ca_cb bond parameters from input file. However, I cannot find which layers this flag belongs to. What’s the key word should I put before the flag in the option file? -
March 11, 2011 at 4:20 pm #5162
Anonymous
what applications assume centroid input (cluster seems to), versus which assume fullatom input (fixbb must)
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March 14, 2011 at 1:25 pm #5171
Anonymous
dock_mcm is still in the docking demo, even though it was deprecated before 3.1…
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March 21, 2011 at 2:23 pm #5208
Anonymous
http://www.rosettacommons.org/content/meaning-totalscore-docking
Fnat appears to be “fraction of native contacts”
I_sc is “interface score” = interaction energy
Irms = interface RMSD
I find no reference to “fa_ hack” or “fa_hack” in the code.
interchain_contact is some sort of filter on whether or not the chains are in contact.
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March 29, 2011 at 7:02 pm #5261
Anonymous
constraints with relax mode: you have to pass all four of these flags:
cst_file
cst_fa_file
cst_weight
cst_fa_weight (not sure about this)to get it to work. This is counterintuitive and should probably be fixed in the code, not documentation.
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March 30, 2011 at 2:48 pm #5266
Anonymous
“When using the cluster application in v3.2, the option -cluster:input_score_filter has no effect.”
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April 19, 2011 at 1:45 pm #5455
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August 2, 2011 at 10:17 pm #5934
Anonymous
How to control input/output types (probably running options too) for jd2 applications. (c.f. http://www.rosettacommons.org/content/question-about-scoring-silent-output-files-and-their-contents)
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August 2, 2011 at 10:19 pm #5935
Anonymous
Which options to use for various input/output types for jd2 applications (common options to control jd2 running wouldn’t hurt either). (c.f. http://www.rosettacommons.org/content/question-about-scoring-silent-output-files-and-their-contents)
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October 11, 2011 at 7:48 am #6120
Anonymous
In “Simple Protocol Walkthrough”: There is no reference to the actual location or names of the files this tutorial is based on. Presumably, the term FILE right in the first paragraph (“the protocol itself is at FILE”) has simply never been replaced.
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March 9, 2011 at 11:25 pm #5149
Anonymous
(archiving the answer, which turned out to be:)
The option is called -packing:preserve_c_beta; the documentation is wrong.
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February 4, 2012 at 3:43 pm #6619
Anonymous
“When using the cluster application in v3.2, the option -cluster:input_score_filter has no effect.”
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Name: lashondaread
Website:nespresso
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