My software notes

December 23, 2010

Install Rosetta-3.1 and CS-Rosetta on Mac OS 10.6

Filed under: mac,softwares and scripts — kpwu @ 7:27 pm
Tags: , , ,

A note of my installation in the last 3 days.

Machine: iMac 3.06 GHz, core i3, 4 GB Ram , OS 10.6.4

Part A –Rosetta 3.1

First download Rosetta 3.1, all the bundle stuff.
–uncompress the bundle file, and keep uncompressing all “.tgz” files
Then download corrections for rosetta_source at here: http://zinc.ucsf.edu/~colin/snow_leopard_tools.tar.gz
(see this discussion topic at Rosetta forum : node 1705)
–go to rosetta_source, uncompress the snow_leopard_tool.tar.gz and the uncompressed files will automatically overwrite the files.

— use “scons” to compile and install by command: “scons bin mode=release”

The compilation takes approximately 1 hour.

NOTE: For Mac users, you can install scons by using Fink.

Second, you need g77 to compile the rosetta_fragments, but even using the unstable packages provided in fink, the x86_64 version of g77 for  OS 10.6 is not available. I went to “high performance computing for mac os X”  to download g77-3.4 which is a binary file already. No need to compile it by yourself.
(I tried gfortran, a lot of errors occurred, but g77 does good job).

After getting g77 works, go to resetta_fragments/nnmake and type make to have pNNMAKE.gnu compiled. This is required for CS-Rosetta,too.

Part B–CS-Rosetta

First, download the all required compressed file at CS-Rosetta official site.
–chmod 711 install.com if this is not executable.
— run ./install.com and the script will ask you to provide the full path of your rosetta-3.1 (not the path of rosetta_source).

You should see error messages that the install script cannot find some Rosetta executable files and my solution is to make soft links at “rosetta_source/bin”

Do this soft link before installing CS-rosetta.

ln -s AbinitioRelax.macosgccrelease AbinitioRelax.linuxgccrelease
ln -s extract_pdbs.macosgccrelease extract_pdbs.linuxgccrelease

— After installation, you should see something like “no errors found” and put the environmental setup in your csh or tcsh and source/update the shell.

To test the CS-Rosetta, I directly go to examples/input, type: runCSRjob3.com gb3.tab and I got:

===============

usersxxx:input>runCSRjob3.com gb3
gb3.pdb gb3.tab
lusersxxx:input>runCSRjob3.com gb3.tab
pre-checking input chemcial shift data …
*** Shift outlier: 14 G C Secondary Shift: -3.765 Limit: -3.725
*** Shift outlier: 15 E HA Secondary Shift: 1.313 Limit: 1.047
*** Shift outlier: 17 T HA Secondary Shift: 1.498 Limit: 1.047
*** Shift outlier: 19 K HA Secondary Shift: 1.070 Limit: 1.047
*** Shift outlier: 25 T CA Secondary Shift: 4.791 Limit: 4.660
*** Shift outlier: 27 E HA Secondary Shift: -1.698 Limit: -1.080
*** Shift outlier: 29 A C Secondary Shift: 4.021 Limit: 3.727
*** Shift outlier: 35 N C Secondary Shift: 4.104 Limit: 3.727
*** Shift outlier: 51 T HA Secondary Shift: 1.197 Limit: 1.047
*** Shift outlier: 52 F HA Secondary Shift: 1.164 Limit: 1.047
*** Shift outlier: 54 V CA Secondary Shift: -4.355 Limit: -3.445
*** Shift outlier: 56 E N Secondary Shift: 10.828 Limit: 10.047
*** C shift referecing offset: -1.289 ppm
Checking and preparing files …
MFR fragments searching … (may take a few hours…)
Done! MFR fragment tables farg9.t000.mfr.tab and frag3.t000.mfr.tab generated.

Converting to ROSETTA fragments …
9mer fragments …
Checking MFR Fragments Candidates …
200 fragments candidates for target fragment 1-9
200 fragments candidates for target fragment 2-10
200 fragments candidates for target fragment 3-11
200 fragments candidates for target fragment 4-12
200 fragments candidates for target fragment 5-13
200 fragments candidates for target fragment 6-14
200 fragments candidates for target fragment 7-15
200 fragments candidates for target fragment 8-16
200 fragments candidates for target fragment 9-17
200 fragments candidates for target fragment 10-18
200 fragments candidates for target fragment 11-19
200 fragments candidates for target fragment 12-20
200 fragments candidates for target fragment 13-21
200 fragments candidates for target fragment 14-22
200 fragments candidates for target fragment 15-23
200 fragments candidates for target fragment 16-24
200 fragments candidates for target fragment 17-25
200 fragments candidates for target fragment 18-26
200 fragments candidates for target fragment 19-27
200 fragments candidates for target fragment 20-28
200 fragments candidates for target fragment 21-29
200 fragments candidates for target fragment 22-30
200 fragments candidates for target fragment 23-31
200 fragments candidates for target fragment 24-32
200 fragments candidates for target fragment 25-33
200 fragments candidates for target fragment 26-34
200 fragments candidates for target fragment 27-35
200 fragments candidates for target fragment 28-36
200 fragments candidates for target fragment 29-37
200 fragments candidates for target fragment 30-38
200 fragments candidates for target fragment 31-39
200 fragments candidates for target fragment 32-40
200 fragments candidates for target fragment 33-41
200 fragments candidates for target fragment 34-42
200 fragments candidates for target fragment 35-43
200 fragments candidates for target fragment 36-44
200 fragments candidates for target fragment 37-45
200 fragments candidates for target fragment 38-46
200 fragments candidates for target fragment 39-47
200 fragments candidates for target fragment 40-48
200 fragments candidates for target fragment 41-49
200 fragments candidates for target fragment 42-50
200 fragments candidates for target fragment 43-51
200 fragments candidates for target fragment 44-52
200 fragments candidates for target fragment 45-53
200 fragments candidates for target fragment 46-54
200 fragments candidates for target fragment 47-55
200 fragments candidates for target fragment 48-56
Collecting structural information … Done (2908)!
Creating Rosetta fragments … Done!
3mer fragments …
Checking MFR Fragments Candidates …
200 fragments candidates for target fragment 1-3
200 fragments candidates for target fragment 2-4
200 fragments candidates for target fragment 3-5
200 fragments candidates for target fragment 4-6
200 fragments candidates for target fragment 5-7
200 fragments candidates for target fragment 6-8
200 fragments candidates for target fragment 7-9
200 fragments candidates for target fragment 8-10
200 fragments candidates for target fragment 9-11
200 fragments candidates for target fragment 10-12
200 fragments candidates for target fragment 11-13
200 fragments candidates for target fragment 12-14
200 fragments candidates for target fragment 13-15
200 fragments candidates for target fragment 14-16
200 fragments candidates for target fragment 15-17
200 fragments candidates for target fragment 16-18
200 fragments candidates for target fragment 17-19
200 fragments candidates for target fragment 18-20
200 fragments candidates for target fragment 19-21
200 fragments candidates for target fragment 20-22
200 fragments candidates for target fragment 21-23
200 fragments candidates for target fragment 22-24
200 fragments candidates for target fragment 23-25
200 fragments candidates for target fragment 24-26
200 fragments candidates for target fragment 25-27
200 fragments candidates for target fragment 26-28
200 fragments candidates for target fragment 27-29
200 fragments candidates for target fragment 28-30
200 fragments candidates for target fragment 29-31
200 fragments candidates for target fragment 30-32
200 fragments candidates for target fragment 31-33
200 fragments candidates for target fragment 32-34
200 fragments candidates for target fragment 33-35
200 fragments candidates for target fragment 34-36
200 fragments candidates for target fragment 35-37
200 fragments candidates for target fragment 36-38
200 fragments candidates for target fragment 37-39
200 fragments candidates for target fragment 38-40
200 fragments candidates for target fragment 39-41
200 fragments candidates for target fragment 40-42
200 fragments candidates for target fragment 41-43
200 fragments candidates for target fragment 42-44
200 fragments candidates for target fragment 43-45
200 fragments candidates for target fragment 44-46
200 fragments candidates for target fragment 45-47
200 fragments candidates for target fragment 46-48
200 fragments candidates for target fragment 47-49
200 fragments candidates for target fragment 48-50
200 fragments candidates for target fragment 49-51
200 fragments candidates for target fragment 50-52
200 fragments candidates for target fragment 51-53
200 fragments candidates for target fragment 52-54
200 fragments candidates for target fragment 53-55
200 fragments candidates for target fragment 54-56
Collecting structural information … Done (4027)!
Creating Rosetta fragments … Done!

Generating ROSETTA path file …
Generating ROSETTA running script …

Fragment Candidates Ready!
Go to rosetta, and type runRosetta3.com to run ROSETTA(3.X)!

===================

However, when I go to the just generated rosetta folder and run “runRosetta3.com”, I got errors:

usersxxx:rosetta>runRosetta3.com
ERROR: Option matching -in::file::frag3 not found in command line top-level context

—> I checked the Rosetta 3 command list and edit the “runRosetta3.com”, replace all double colons “::” by single colons “:” and save it. The edited “runRosetta3.com” is running now.

–> After testing, taking off one colon is necessary to run CS-rosetta well on my iMac.

12/23/2010

update: 1/27/2011

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8 Comments »

  1. Thanks once more for this nice and easy way how to install Rosetta in Mac OS X.
    Is really a nice tutorial. I have follow that and managed to install Rosetta on my Mac OS X 10.5.8, however I have a problem when test the CS-Rosetta by runCSRjob3.com gb3.tab in examples/input folder:

    pre-checking input chemcial shift data …
    *** Shift outlier: 14 G C Secondary Shift: -3.765 Limit: -3.725
    *** Shift outlier: 15 E HA Secondary Shift: 1.313 Limit: 1.047
    *** Shift outlier: 17 T HA Secondary Shift: 1.498 Limit: 1.047
    *** Shift outlier: 19 K HA Secondary Shift: 1.070 Limit: 1.047
    *** Shift outlier: 25 T CA Secondary Shift: 4.791 Limit: 4.660
    *** Shift outlier: 27 E HA Secondary Shift: -1.698 Limit: -1.080
    *** Shift outlier: 29 A C Secondary Shift: 4.021 Limit: 3.727
    *** Shift outlier: 35 N C Secondary Shift: 4.104 Limit: 3.727
    *** Shift outlier: 51 T HA Secondary Shift: 1.197 Limit: 1.047
    *** Shift outlier: 52 F HA Secondary Shift: 1.164 Limit: 1.047
    *** Shift outlier: 54 V CA Secondary Shift: -4.355 Limit: -3.445
    *** Shift outlier: 56 E N Secondary Shift: 10.828 Limit: 10.047
    *** C shift referecing offset: -1.289 ppm
    Checking and preparing files …
    MFR fragments searching … (may take a few hours…)
    Done! MFR fragment tables farg9.t000.mfr.tab and frag3.t000.mfr.tab generated.

    Converting to ROSETTA fragments …
    9mer fragments …
    Can’t open file frag9.t000.mfr.tab for reading
    ERRORS found for fragment candidates, quit …

    the Rosetta stops. Do you have any idea what is going on?
    The Rosetta build has shown some warning messages, but at the end didn’t find any errors.

    Example of a warning message:
    -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/macos/64/gcc -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/forge/methods/fold_tree_functions.cc
    src/protocols/forge/methods/fold_tree_functions.cc: In function ‘void protocols::forge::methods::make_star_foldtree(core::pose::Pose&, protocols::loops::Loops)’:
    src/protocols/forge/methods/fold_tree_functions.cc:1152: warning: comparison between signed and unsigned integer expressions
    src/protocols/forge/methods/fold_tree_functions.cc:1154: warning: comparison between signed and unsigned integer expressions

    The CS-Rosetta was also installed with “no errors found”
    Do you have any ideas what is going on? If you could help I would be grateful.

    Cheers.

    Comment by Angelo — January 27, 2011 @ 6:45 am | Reply

    • Hello Angelo,

      Unfortunately, I don’t really know what happened to you case. I do remember one time that I used one published assignment table from BMRB (~10 kD) to test CS-rosetta, the program returned me that the sequence was not found and stopped. Actually the sequence was not copied into the working folder for rosetta (e.g. project_xx/rosetta).

      Your case seems to be related to the rosetta_fragment. I would try to recompile the rosetta_frag using g77 (from the binary file I provided) and reinstall cs-rosetta again.

      hope that’s helpful.
      kp

      Comment by kpwu — January 27, 2011 @ 6:31 pm | Reply

  2. OK, here is the answer to sort out the problem.
    According to Yang Shen this problem some times happens in certain MacOSX, the trick to resolve it is removing the ‘problematic’ protein(s) from the database, so what you have to do according to Y.Shen is:

    “1. find the “$CSROSETTA_DIR/PDBH/resolution.tab” and open it with any text editor.

    2. find the protein in the “resolution.tab” file which is next to the last ‘good’ protein in the “t000.mfr.log file”, for example, 1I1QA.pdb is the “problematic” one next to the “1I1NA.pdb”, which is the last protein searched by MFR in your system.

    3. remove this protein in the “resolution.tab” file (or put a “#” character in the begining of the line containing the “problematic” protein).

    4. re-run the fragment searching (“runCSRjob3.com gb3.tab”).

    Another user also mentioned another “problemaic” protein “1MTYD.pdb”, for which you may need to remove it as well if you like to try this method.”

    Comment by Angelo — February 1, 2011 @ 7:36 am | Reply

    • Thank you, Angelo. Glad to know how to solve this problem!

      Comment by kpwu — February 2, 2011 @ 2:09 pm | Reply

  3. Thanks to your blog, I could successfully installed rosetta and cs-rosetta. I really appreciate it.

    Comment by Daisuke Takahashi — August 31, 2011 @ 5:22 pm | Reply

  4. Error: /home/ashutosh/csrosetta/src/mfr2rosetta/mfr2rosetta is not found. mfr2rosetta compilation failed
    I am getting problem at this stage , even I did manually set the script of csrosettalnit.com, set environment of all variables but its showing same error at all the time.

    if you have any idea for this problem, please share with us ..I would be grateful .

    Comment by arpit katiyar — June 10, 2013 @ 3:58 pm | Reply

    • I think you better to ask Rosetta experts or CS-Rosetta author. I don’t know what causes this issue from the limited information. Cheers.

      Comment by kpwu — June 11, 2013 @ 1:48 am | Reply

  5. Hi
    I am working on Cs-rosetta on Ubuntu. I am getting error at the rescoring stage.

    % runCSrescore3.com default.out bal.tab
    ./output directory generated

    extracting PDB coodinates…

    generate decoys raw score table file : ./output/name.rawscore.txt
    rescoring decoys using sparta calculated chemical shifts…
    (input chemical shift shift bal.tab )
    foreach: No match.
    %

    how can I solve this error?

    Comment by Kumud Agarwal — January 23, 2014 @ 3:01 am | Reply


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