Blast and Genome database requirement is compusory in rosetta w52 release

[Anonymous]

Hello sir, I am installing rosetta w52 release, when i install Toolbox, it is automatically downloading the NMRPipe, Blast and Genome Database from nih site, and this process taking day by day, so please tell me is this compulsory for this or not??

[Anonymous]

You shouldn’t need it unless you are doing fragments-based work (ab initio, CSRosetta, that sort of thing). What part of the toolbox do you need?

[Anonymous]

Hello rmoretti thanks for helping

I am running Rosetta3.5 Week 52, when I run tutorial_pick_fragment.sh in the rosetta3, tutorial folder, it generates one folder-> Pick_fragment containing many files, these are 2jrm.tab, 2jrm.bmrb, 2jrm_trim.fasta and two fplder also but they all are the empty exept 2jrm.bmrb and the same happened when I run command bmrb2talos only empty .tab file created so what is the problem in the program I am not Understanding please help if u can do???
So please You or anyone can tell me step by step from starting how to initiate working with rosetta, at initial stage like first time user, because I does not know anything more…..
like……
What are commands..??
where I have to give command ??
What are the required scripts..?
ex. bmrb to tab conversion
renumbering of peptide
etc….

Thank You

[Anonymous]

Thank You smlewis,
I have done both W52 package compilation and toolbox2.0 installation in the system and at the end messege came like, installation done succesfully.
but when I am trying file conversion from .bmrb to .tab using command as below an error has occured

user@user-HCL-Desktop:~$ ls
csrosetta3 examples.desktop NMR_Pipe_7.9 project.git Ubuntu One
Desktop fid.com NMRViewJ Public Videos
Documents kk-rosetta nvjinstall8_0_3.jar rosetta zlib-1.2.8
Downloads Music Pictures Templates
user@user-HCL-Desktop:~$ cd kk-rosetta
user@user-HCL-Desktop:~/kk-rosetta$ ls
2jrm_trim.fasta bmrb2talos.com ner103a.bmrb ner103a.tab renumber_talos.py
user@user-HCL-Desktop:~/kk-rosetta$ csh
% ls
2jrm_trim.fasta bmrb2talos.py ner103a.tab SgR145.fasta
bmrb2talos.com ner103a.bmrb renumber_talos.py
% ./bmrb2talos.py ner103a.bmrb > ner103a.tab
Traceback (most recent call last):
File “./bmrb2talos.py”, line 29, in
from basic.options import ExampleArgumentParser
ImportError: No module named basic.options
% bmrb2talos.py ner103a.bmrb > ner103a.tab
Traceback (most recent call last):
File “bmrb2talos.py”, line 29, in
from basic.options import ExampleArgumentParser
ImportError: No module named basic.options
%

So, please tell me the next step after installation these, if here required, and why this error came…….

Thank You…

[Anonymous]

The problem you’re having is that Python doesn’t know where to find the modules for Rosetta. It needs to be informed of the Rosetta and CS Rosetta installation paths.

When you installed CS Rosetta, it should have generated initialization scripts in the csrosetta3 directory – both init.bashrc and init.cshrc. You should source one of those into your current shell prior to starting any CS Rosetta work. This will set up the paths for Python as well as for other items.

For your example, immediately after you ran “csh”, you should do something like “. ~/csrosetta3/init.cshrc”, substituting the appropriate path for the “~/csrosetta3/init.cshrc”. The dot-space syntax tells the shell to execute the script and load the resultant environment changes into the current environment (roughly speaking). That syntax works for both Bash and C shells – just change which script you use. If you find it a hassle to do this every time, simply add a line doing to to your ~/.cshrc or ~/.bashrc shell initialization file.

[Anonymous]

Thank You rmoretti, yes i found these files as you told….. but again I am facing problem in starting the work on rosetta like this

1. Error in init command….

user@user-HCL-Desktop:~$ cd csrosetta3
user@user-HCL-Desktop:~/csrosetta3$ init.cshrc
init.cshrc: command not found
user@user-HCL-Desktop:~/csrosetta3$ ./init.cshrc
bash: ./init.cshrc: No such file or directory
user@user-HCL-Desktop:~/csrosetta3$ cd com
user@user-HCL-Desktop:~/csrosetta3/com$ ls
annotate_target.py fasta2weight.py renumber_prot.py
autoNOE_select_final_run.py get_rdc_tensor.py renumber_rdc.py
bmrb2fasta.py init renumber_talos.py
bmrb2prot.py init.bashrc renumber_upl.py
bmrb2rdc.py init.cshrc rosetta2upl.py
bmrb2talos.py install.py setup_autoNOE.py
clean_peak_file.py list_setup.py setup_display.py
clean_rdc_file.py median.py setup_list.py
convert_atomnames.py noeout2txt.py setup_run.py
correctCSoffset.py pack_pdbs.py setup_target.py
cst_map_toCB.py pdb2fasta.py silent_data.py
cst_map_toCEN.py pick_fragments.py talos2fasta.py
display_setup.py pred2rigid.py talos2prot.py
extract_decoys.py process_prot_for_autoNOE.py unpack_pdbs.py
extract_scores.py prot2talos.py upl2fasta.py
fasta2seq.py renumber_pdb.py upl2rosetta.py
user@user-HCL-Desktop:~/csrosetta3/com$ ./init.bashrc
bash: ./init.bashrc: Permission denied
user@user-HCL-Desktop:~/csrosetta3/com$ init.bashrc
init.bashrc: command not found
user@user-HCL-Desktop:~/csrosetta3/com$ ./init.cshrc
bash: ./init.cshrc: Permission denied
user@user-HCL-Desktop:~/csrosetta3/com$

2 Error in converting file

user@user-HCL-Desktop:~$ ls
cns_solve_1.21 Downloads Music project.git Videos
cns_solve_1.3 examples.desktop NMR_Pipe_7.9 Public zlib-1.2.8
csrosetta3 fid.com NMRViewJ rosetta
Desktop haddock2.1 nvjinstall8_0_3.jar Templates
Documents kk-rosetta Pictures Ubuntu One
user@user-HCL-Desktop:~$ cd csrosetta3
user@user-HCL-Desktop:~/csrosetta3$ ls
2jrm.bmrb com database frag_picker kk-rosetta python tutorials
2jrm.tab com_alias flag_library install.py NMRPipe tests
user@user-HCL-Desktop:~/csrosetta3$ cd kk-rosetta
user@user-HCL-Desktop:~/csrosetta3/kk-rosetta$ ls
2jrm_trim.fasta bmrb2talos.py init.cshrc renumber_talos.py
bmrb2talos.com init.bashrc ner103a.bmrb SgR145.fasta
user@user-HCL-Desktop:~/csrosetta3/kk-rosetta$ bmrb2talos.py ner103a.bmrb > ner103a.bmrb
bmrb2talos.py: command not found
user@user-HCL-Desktop:~/csrosetta3/kk-rosetta$ csh
% bmrb2talos.py ner103a.bmrb > ner103a.tab
Traceback (most recent call last):
File “bmrb2talos.py”, line 29, in
from basic.options import ExampleArgumentParser
ImportError: No module named basic.options
% ./bmrb2talos.py ner103a.bmrb > ner103a.bmrb
Traceback (most recent call last):
File “./bmrb2talos.py”, line 29, in
from basic.options import ExampleArgumentParser
ImportError: No module named basic.options

So u can tell me , Is there the csrosetta3 toolbox installation folder in Home directory or inside the Rosetta main package, now I have both of these in Home directory ……..

and please tell me the specific executable command for the starting the rosetta…

Thank you…..

[Anonymous]

Sorry about that — you’re right that the init files are in ~/csrosetta3/com/ rather than just ~/csrosetta3/

The reason the initialization script isn’t working for you is that you need to *source* the script in your shell, rather than just run it. When you run a script normally, any changes to the environment the script makes aren’t made to the parent shell – they only exist while the script is running, and only for that script and the programs it launches.

$ init.bashrc ## This doesn’t work because the shell tries to search for the command “init.bashrc” in the standard executable directories (your $PATH settings) – ~/csrosetta3/com/ isn’t in your path, so it can’t find it.
$ ./init.bashrc ## While this tells the shell to look in the current directory for the script, this doesn’t work because the script isn’t marked as being executable. Being marked as executable doesn’t matter for this script as, again, you don’t want to run it, you want to *source* it.

What you should be doing is:

$ . ./init.bashrc ## Note the space between the dot and the filename. That first dot isn’t part of the path of the script, it’s a built-in shell command saying “source the following file, rather than running it”. I’ve added the “./” here to make it clear that that first dot isn’t part of the filename/path

On many shells you can use the more mnemonic “source” command as opposed to “.”

$ source ./init.bashrc

The availability of the “source” built-in command as an alias for the “.” command is somewhat shell dependent. Bash allows it, and some versions of tcsh allow it, but it’s far from universal.

The errors you see in 2. are a result of not having the environment variables set from your initialization script. The initialization scripts, when properly sourced, should set up your shell environment appropriately (specifically, setting the $PYTHONPATH) such that Python will be able to find the Rosetta modules, and you shouldn’t get the basic.options ImportError.

[Anonymous]

I’m not familiar with the tutorial_pick_fragment.sh script you mention. Where exactly did you obtain it from?

At any rate, if you’re interested in using CSRosetta fragment picking, I’d highly recommend becoming familiar with the materials at http://www.csrosetta.org/tutorials and http://www.csrosetta.org/node/1339 as well as the other manuals and guides at that site. (There’s even a CSRosetta specific forum there – which if you’re having issues with the CSRosetta specific scripts might be a good resource, as the experience of people herewith the CSRosetta-specific stuff is limited.)

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