My software notes

December 27, 2010

Test reports of CS-Rosetta (3.1)

Filed under: mac,softwares and scripts,xplor/xplor-nih/cns — kpwu @ 1:08 pm
Tags: , ,

On Dec 23rd, I successfully install Rosetta 3.1 and CS-Rosetta on my iMac and run the test using GB3 protein which was provided within the CS-Rosetta.

Here are the rough steps I used to get a simulated GB3 protein.

  1. run “runCSRjob3.com” as instructed in the online manual
  2. The RunRosetta3.com has to be modified first to perform ab initio simulation by Rosetta3.
    (basically, just replace all double colon “::” in the RuRosetta3.com by single colon “:”).
  3. After ~70 hours simulation using a single CPU (3.06 GHz) on my iMac, I got the simulation done.
  4. As instructed by CS-Rosetta, one has to generate a “silent output” (the extract_lowscore_decoys.py).
  5. Before running “runCSrescore3.com”, you have to edit 2 files:
    1. go to the CS-Rosetta folder, in the “com” subfolder,edit “extract_pdb3.com”, make sure no double colons are in the script same as step 3.
    2. edit runCSrescore3.com,:
    at line 28, it was “mkdir output -p” and the new one should be “mkdir -p output”,
    at line 101, it was “rm ./pred/………  -f” and the new one should be “rm -f ./pred…….”.
    Then you can run “runCSrescore3.com” and no error/warming messages will be shown.

I don’t give the program the defined seg.txt in this test.

The error message at step 5.2 look like the following lines:

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

userssxx:rosetta>runCSrescore3.com new_silent.out
./output directory generated
mkdir: output: File exists
mkdir: -p: File exists

extracting PDB coodinates…

generate decoys raw score table file : ./output/name.rawscore.txt
decoy with the lowest energy score: S_j001_00000289
calculate rmsd to the lowest raw score decoy ( S_j001_00000289 ) and generate file : ./output/rms2LowRawScore.txt
generate rms_toLowestRawscoreModel verus score table file : ./output/name.rms.rawscore.txt
labadmin:rosetta>runCSrescore3.com new_silent.out gb3.tab
./output directory generated
mkdir: output: File exists
mkdir: -p: File exists

extracting PDB coodinates…

generate decoys raw score table file : ./output/name.rawscore.txt
rescoring decoys using sparta calculated chemical shifts…
(input chemical shift shift gb3.tab )
calculating chemical shift score for decoy S_j001_00000001
rm: -f: No such file or directory
calculating chemical shift score for decoy S_j001_00000002
rm: -f: No such file or directory
calculating chemical shift score for decoy S_j001_00000003
rm: -f: No such file or directory

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

Now, I am waiting for the back CS-prediction by Sparta and getting the scores. But I check several simulated PDB coordinates of GB3 protein, the structures are quite similar with the published one. Here is a random one.

After the complete of back CS prediction by sparta, the script RunCSrescore3.com is supposed to collect all information and generate few text file which contains the CS_chi2, rms and other information. I don’t know why the script was looking for S_j001_0001000.pdb (because I don’t have it, only 0-999.pdb), so the “pdbrms doesn’t work properly. Therefore name.rms.rescore.txt” does not have the complete information (should have 3 columns).

I did the following steps to get the complete information. All the following commands are extracted from the runCSrescore3.com

  1. set best_model = `cat name.rescore.txt | sort -g -k4 | head -n1 | awk ‘{print $1}’`
  2. pdbrms $best_model.pdb S*.pdb | awk ‘{print $2,$1}’ | sort -g > rms2LowReScore.txt
    if you have seg.txt, then the commands are:
    set seg = `cat ../seg.txt`
    pdbrms $best_model.pdb S*.pdb -seg $seg | awk ‘{print $2,$1}’ | sort -g > rms2LowReScore.txt
  3. paste name.rescore.txt rms2LowReScore.txt | awk ‘{ print $1,$6,$4 }’ > name.rms.rescore.txt

The 1000 simulated GB3 structures seem to have trend of convergence (see the figure below). If more structures as suggested by the CS-rosetta manual (e.g. 10,000 structures), the convergence should be clear.

The 20 lowest Calpha_RMSD structures (left) and 20 lowest energy structures are superimposed by the NMR plugin in pymol which RMSD of backbone atoms (residues 1-56) are 0.6  and 0.68 angstrong, respectively.

December 24, 2010

Install Xplor-NIH 2.26 on new iMac (10.6)

Filed under: mac,softwares and scripts,xplor/xplor-nih/cns — kpwu @ 9:52 am
Tags: , ,

A short note for installation of xplor-nih 2.26 on iMac.

Few months ago, I downloaded XPLOR-NIH 2.26 for Mac OS and installed it on my new iMac (core i3, 3.06 GHz). The default configuration script does not include “Intel Core i3”  in the processor list (at xplor-nih-xxx/arch/getDarwinCPU).

The solution to make the configuration is to edit “getDarwinCPU” script. I replaced i5 by i3 at line 21 and keep everything else unchaged.  The configuration script works and an extensive test were performed, no interruption occurred.

Second note on 2/5/2011.
For version of Xplor-NIH 2.27, same edition has to be done to make it run well on my iMac. Some Mac users may have the same problem.
 

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

Blog at WordPress.com.