1. How can I get a Rosetta software license?
2. What is RosettaDesign?
3. What is RosettaDock?
4. What is Ab inito folding?
5. What is the difference between Ab Initio and De Novo Modeling?
6. What is RosettaNMR?
7. What is RosettaLigand?
8. What are Fragment Libraries?
9. Which compiler should I use to build rosetta software?
10. How do I interpret the energies output by Rosetta?
11. How to cite ROSETTA in papers?
12. Where is Rosetta software documentation?
13. What's the minimum and recommended hardware settings for Rosetta software?
14. Does the Rosetta software come as pre-compiled executables, or source code, in which language?
15. What should I do if I have missing backbone atoms at residues in my pdb file?
16. Where can I find createTemplate.pl?
17. Is there somewhere I can see the rosetta options/flags/arguments for the commands?
18. Are there any protocols or functions in Rosetta that use MPI directives or do you have to parallelize the code by sending multiple jobs?
19. What is the value of Temperature which is used in Rosetta simulations?
20. I could not find the file named "pNNMAKE.gnu" which is used when I run make_fragments.pl to create fragments.
21. Is there a manual for Rosetta Docking?
22. How can I install rosetta on windows XP?
23. How can I do multiple chains fixed backbone design?
24. I'm wondering whether Rosetta is known to build and run on Linux/IA64 platforms?
25. How to compile Rosetta on an intel mac?
26. What is a FASTA file?
27. How can I create a fragment file?
28. What is the difference between a .cst file and and .dst file, if any? Are the formats the same?
29. What is "unrecognized residue:"?
30. What is the difference between redesigning on a fixed backbone and repacking on a fixed backbone?
31. The run terminates without generating any structures. Why?
32. Rosetta is unable to find my input files. What's wrong?
33. What's all this stuff in the fragment files?
34. What's in the .cshft file?
35. What are all these files that are included with the fragments?
36. How come rosetta is reporting rms to the native structure when there is no native structure?
37. Rosetta completely messes up my CNS structure. Why?
38. Why are three-state psipred files (.psipred_ss2) not being read in correctly?
39. I'm using NOE constraints and Rosetta is running REALLY slowly. What's up?
40. How can I get coordinates for the fragments in my fragment libraries?
Answers
Q: How can I get a Rosetta software license?
A:
Rosetta is available to academic and commercial researchers through a license. please check the following link for more information: http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rose... link
Q: What is RosettaDesign?
A:
RosettaDesign? identifies low energy sequences for specified protein backbones, and has been used previously to stabilize proteins and create new protein structures. Please visit our RosettaDesign? server: http://rosettadesign.med.unc.eduexternalexternal link link
Q: What is RosettaDock?
A:
RosettaDock? predicts the structure of a protein-protein complex from the individual structures of the monomer components. Visit our RosettaDock? server: http://graylab.jhu.edu:8088/externalexternal link link
Q: What is Ab inito folding?
A:
Ab initio protein folding performs task of predicting 3-D structural models for a protein molecule from its sequence information. visit our full-chain protein structure prediction server: Robetta: --- http://robetta.org/external link
Q: What is the difference between Ab Initio and De Novo Modeling?
A:
Ab initio structure prediction classically refers to structure prediction using nothing more than first-principles (i.e. physics). De Novo is a more general term that refers to the greater category of methods that do not use templates from homologous PDB structures. Since Rosetta uses fragments from existing PDB structures in order to guide the search in conjunction with energy functions, there is a semantic argument as to whether it is truly "ab initio" (although the same could be said for any statistically derived energy function). Long story short: call it what you want, but be prepared for a debate!
Q: What is RosettaNMR?
A:
RosettaNMR combines the Rosetta de novo structure prediction method with limited experimental data from NMR for rapid prediction of protein structure. NMR constraints of RDC and NOE have been used successfully in RosettaNMR to determine global folds.
Q: What is RosettaLigand?
A:
RosettaLigand? employs the full atom modes of Rosetta to predict the interactions of protein-small molecule interactions.
Q: What are Fragment Libraries?
A:
Fragment Libraries are the pieces of experimentally determined structures that Rosetta uses to guide the search of conformational space when predicting structures using the ab initio protocol, as well as longer loop conformations in homology models.
Q: Which compiler should I use to build rosetta software?
A:
We suggest gcc-3.4.x for the latest rosetta release.
Q: How do I interpret the energies output by Rosetta?
A:
Please check the following link which can help you to understand Rosetta results. http://www.rosettacommons.org/tiki/tiki-index.php?page=Design#_b_Interpr... link
Q: How to cite ROSETTA in papers?
A:
The place to find Rosetta-related publications currently is http://www.rosettacommons.org/publications/externalexternal link link
Q: Where is Rosetta software documentation?
A:
You can find a neat user guide in the following link. You can also download the rosetta_documents package from the release links with more detailed examples and instructions. http://www.rosettacommons.org/tiki/tiki-index.php?page=User+Guide+for+Ro... link
Q: What's the minimum and recommended hardware settings for Rosetta software?
A:
single processor computer should be fine, the faster the better. We recommend at least 1G memory for best performance.
Q: Does the Rosetta software come as pre-compiled executables, or source code, in which language?
A:
We distribute source code in C++ and users need to compile it themselves.
Q: What should I do if I have missing backbone atoms at residues in my pdb file?
A:
rosetta can not handle residues with missing backbone atoms. You can use the script "pdb_remove_missing_bb.pl" to remove residues with incomplete backbones, which is in the rosetta_script directory. Another way to solve this problem is that you can add "-skip_missing_residues" in your command line.
Q: Where can I find createTemplate.pl?
A:
You can find an optional package named BioTools? in the software download page. The createTemplate.pl is in this package.
Q: Is there somewhere I can see the rosetta options/flags/arguments for the commands?
A:
Yes, you can find all the rosetta options in a file named "README.options_list" in the directory rosetta_documents.
Q: Are there any protocols or functions in Rosetta that use MPI directives or do you have to parallelize the code by sending multiple jobs?
A:
There is MPI support in Rosetta, though this has not been tested with Condor. MPI is included for PBS-style supercomputers which allocate a large number of nodes at once. For a Condor cluster, MPI is not needed to run Rosetta in parallel - due to the "embarrassingly parallel" nature of the jobs, there would be no advantage. Instead, simply submit all the jobs as single independent jobs on Condor.
Q: What is the value of Temperature which is used in Rosetta simulations?
A:
The temperature unit is Kcal/(mol*K), here K is the Boltzmann constant.Rosetta simulate annealing starts with Kt= 300 and ends at Kt=0.3.
Q: I could not find the file named "pNNMAKE.gnu" which is used when I run make_fragments.pl to create fragments.
A:
pNNMAKE.gnu is not a pre-existed file. You need generate it after you download the rosetta_fragments package. After entering the rosetta_fragment/nnmake directory, type "make" to compile and the pNNMAKE file will be generated.
Q: Is there a manual for Rosetta Docking?
A:
There is a docking tutorial in the rosetta++2.1 package. You should find it in the path rosetta_documentation/docking/tutorial. Analso in the following link. http://graylab.jhu.edu/~mdaily/tutorial/externalexternal link link
Q: How can I install rosetta on windows XP?
A:
There is an instruction for building rosetta on windows named README.VC2005.BuildExample in released 2.2.0 package. It requires the VC2005 installed on your windows system.
Q: How can I do multiple chains fixed backbone design?
A:
Use -read_all_chains in your command line if you want to input a structure with multiple chains. Otherwise, rosetta will only read the first chain of the pdb file.
Q: I'm wondering whether Rosetta is known to build and run on Linux/IA64 platforms?
A:
We do not guarantee that rosetta++ works with 64bit system at this moment. But you still can try to built rosetta++ as a 32bit application on 64bit machines. You need to use "make gcc64" to build the target with the correct version of zlib data compression library for your system, and you need to modify the makefile to direct to the correct path to your library.
Q: How to compile Rosetta on an intel mac?
A:
Check the following link and you can find out how Rosetta++ builds on macs. http://www.rosettacommons.org/tiki/tiki-index.php?page=Compiling+Rosetta... link
Q: What is a FASTA file?
A:
FASTA (sequence) file> (.fasta) The sequence description. Specified by the 9th line of paths.txt (see the section called ths (text)-1òý) Format: See the section called "Sequences (FASTA)". ult: .fasta in the directory specified by paths.txt. There is no way to change the name expected
Q: How can I create a fragment file?
A:
We highly recommendate that use Robetta server to create fragment file. http://robetta.bakerlab.org/fragmentsubmit.jsp.externalexternal link link
Q: What is the difference between a .cst file and and .dst file, if any? Are the formats the same?
A:
The formats of *.cst and *.dst file are different. The explanation of the difference is in the docking tutorial. If you have Rosetta 2.1.0 or higher version, the formats are described here: rosetta_documentation/docking/tutorial/constraints.html.
Q: What is "unrecognized residue:"?
A:
The server read the three letters representation of 20 types of amino acids identities from the pdb file. Sometimes, there are one or more identities which are not included in the 20 amino acides shows in the pdb files so that the server can not recognized them.
Q: What is the difference between redesigning on a fixed backbone and repacking on a fixed backbone?
A:
Repacking is one of the steps of redesign. Repacking tries to find the minimum energy between the sidechains, by doing a monte carlo simulated annealing search through the rotamer configurations. Redesign varies which residues are actually packed, as well as doing repacking. You would use repacking to further refine a design you believe to be useful.
Q: The run terminates without generating any structures. Why?
A:
If rosetta cannot open the output pdb files for any reason, it assumes that they already exist and do not need to be made.
The reason for this behavior is so that multiple processors can work on the same batch of structures and not conflict. A side effect, however, is that if process do not terminate normally, zero-length pdb files are left. Rosetta will not overwrite or remove these files. If they exist in your output pdb directory, you should remove them before starting a new process.
A second common reason for this behavior is that directory to which you are trying to write pdb files either does not exist or does not have the correct permissions.
Q: Rosetta is unable to find my input files. What's wrong?
A:
1. Make sure all the paths are set appropriately in paths.txt
2. Make sure you have the proper file names for all components. Read the log file. It should tell you which files rosetta is looking for and where it expects to find them.
3. pdb codes must be 4 characters long
Q: What's all this stuff in the fragment files?
A:
frag files-- fields are 1 frag source pdb 2 chain 3 residue 4 sequence 5 ss type 6-8 phi,psi,omega 9 score 10-11 ca_dme, all_atom_dme to native (diagnostic only) 12 method by which frag scored high enough to be in frag list
1=sam-t99, 2=psipred (jones) 3=phd 4=nmr data 13 score for noes + rdcs 14-end Position X Frag X
Frags ordered by position and frag #, one line per residue with blank lines between frags
naming conventions: cc1d3z_03_05.200_new_d cc arbitrary (user's choice) 1d3z_ pdb code + chain 03 frag size 06 methods for frag selection (05=ss prediction only, 06= +exp data) 200 depth of frag file (200 frags at each position) _new_d method of removing homologs (internal tracking purposes only)
Q: What's in the .cshft file?
A:
1d3z_.chsft --the results of the TALOS search
fields: 1 residue position 2 predicted ss type 3-4 predicted phi/psi 5-6 variance for phi/psi 7-12 phi/psi of three closest matches 13-14 native phi/psi 15-16 std dev on phi/psi 17 best score 18 average score of top ten matches
1. The four lines preceding data in the '.cst' file are required, they are
an indicator of the format type, two lines of comments (the lines must
be there, but the content is arbitrary), and the number of lines in the
file that should be read (ie if you don't want to use all the data, this
could be less than the number of lines in the file.
Also the format of this file must be precisely as described in the
data_formats.README (which is in with all the 1d3z sample files)
Files are parsed by column number, not on whitespace, so if something
is in the wrong column, it will not be read correctly. 2. The raw chemshift data should be called '.cshft_in'. This is input for
the talos search. '.cshft' is output from the talos search 3. The .'chsft_in' file must have one line for each residue in the protein 4. All sequence-derived files should be named by the 4-letter pdb code and
the one letter chain indicator with '_' used for a ' ' chain indicator.
This will pretty much be all files, with the exception of pdb files, which
do not have the chain indicator.
Q: What are all these files that are included with the fragments?
A:
Files returned with fragment files: new files: .chsft results of the talos search, used to pick frags .jones, .rdb, .sam three secondary structure predictions, used to pick frags
.jones will also be used by rosetta
(.psipred is equivalent to .jones; .psipred_ss2 may
replace .jones) .checkpoint parsed profile from a blast search, used to pick frags .homolog_nr homologs to your protein found in the nr .homolog_vall homologs to your protein in the database used to pick frags aaXXXX03_06.200_new_d frag files read by rosetta, these were made with the chemshift aaXXXX09_06.200_new_d and cst data you sent, homologs were NOT excluded
Q: How come rosetta is reporting rms to the native structure when there is no native structure?
A:
Any pdb file named 1abc.pdb (where 1abc is the pdbcode given as an argument at runtime to rosetta) that rosetta finds on the pdb path, will be assumed to be the NATIVE structure. rms's to this structure will be reported in the output. The presence of such a file does not affect how the code runs, but it will affect the 'rms' fields in your logfiles, scorefiles and pdb files.
Q: Rosetta completely messes up my CNS structure. Why?
A:
Any input structures into rosetta (ie with the -s command line option) must be idealized or rosetta will be unable to fold them. This should only be an issue if you're trying to start from a CNS or other structure and refine it with rosetta.
Q: Why are three-state psipred files (.psipred_ss2) not being read in correctly?
A:
Check the format of the .psipred_ss2 files in the distributed examples for proper formatting. Rosetta is expecting the format obtained from Psipred v2.0.1. Later versions may have leading lines at the head of the file that need to be removed.
Q: I'm using NOE constraints and Rosetta is running REALLY slowly. What's up?
A:
First, make sure you have the latest patch to fold_constraints.f.
You should have v1.17.2.2.4.1 (or later) for rosettaNMR-v1_2 and v1.17.2.2.4.1 (or later) for rosettaCOMBINED-v1_2. See the README accompanying the patches for a description of the modifications applied by the patch.
With this version of fold_constraints.f, two folding protocols are available.
The default version is quite slow, (although faster than the unpatched version). This protocol was under development at the time of release and uses minimization in combination with fragment assembly. While slower, it may be more effective for proteins with complex topologies. This protocol has not been published. The original folding protocol published in the Bowers et al J Biomolec NMR article is also now available. This protocol runs MUCH faster than the default protocol.It is accessed by using the '-fast' command-line option.
Second, significant speed advantages can be obtained by trimming your NOE list appropriately.
We typically do not include any short range NOEs: < i, i+9 .
These NOEs should be used in selecting fragments, but for fragment assembly, the information is already inherent in the fragment set, and rosetta does not require many short range constraints to form regular secondary structure.
Q: How can I get coordinates for the fragments in my fragment libraries?
A:
Coordinates for all fragments are precalculated in the vall_cst_coord.dat.* file. The fields in this file are:
1 frag source pdb name 2 frag source chain 3 frag source residue 5-7 HN coords (x,y,z) 8-10 HA coords 11-21 coefficients for evaluating RDC restraints 22-24 N coords 25-27 CA coords 28-30 CB coords 31-33 C coords 34-36 O coords
All fragments in fragment libraries are identified by the frag source pdb name, chain and residues, allowing relevant coordinates to be extracted from the vall_coord_cst.dat.* data file.