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.

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