Collecting 3.2 documentation holes

[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.

[Anonymous]

Executive summary: How does one generate custom fragment libaries from rosetta-annotated sequences / fastas?

http://www.rosettacommons.org/node/2261

[Anonymous]

There is no documentation for the residue_pair_jump_cst file type (metalloprotein_abrelax integration test, read by protocols/jumping/ResiduePairJumpSetup)

[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.

[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.

[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”

[Anonymous]

A) check FloppyTail documentation vs. “publication mode”

ensure that AbinitioRelax does not default to looking for Oliver’s directory for the minirosetta_database

[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?

[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 (!!!!)

[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.

[Anonymous]

Docking partners flag uses underscore to separate groups

[Anonymous]

https://www.rosettacommons.org/node/2332

AbinitioRelax A) produces silent files by default, and suggests nonexisting executeables to convert them to PDB

[sokrypton]

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?

[Anonymous]

what applications assume centroid input (cluster seems to), versus which assume fullatom input (fixbb must)

[Anonymous]

dock_mcm is still in the docking demo, even though it was deprecated before 3.1…

[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.

[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.

[Anonymous]

“When using the cluster application in v3.2, the option -cluster:input_score_filter has no effect.”

[Anonymous]

http://www.rosettacommons.org/content/problem-when-exact-pdb-silent-file

[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)

[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)

[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.

[Anonymous]

(archiving the answer, which turned out to be:)

The option is called -packing:preserve_c_beta; the documentation is wrong.

[Anonymous]

“When using the cluster application in v3.2, the option -cluster:input_score_filter has no effect.”

_______

Name: lashondaread

Website:nespresso

[Author]

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