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fixing sym to work in pyrosetta4 and adding a new fn to help in templ… #2

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275 changes: 275 additions & 0 deletions symmetry/Symmetry Setup Mark II.ipynb
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Original file line number Diff line number Diff line change
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Found rosetta database at: /home/stephanie/anaconda2/envs/DebugPyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/database; using it....\n",
"PyRosetta-4 2016 [Rosetta 2016 unknown:9ea8e5e15e7c35838a32b8089ca8351ff540888c 2016-12-16 10:52:45 -0500] retrieved from: git@github.com:RosettaCommons/main.git\n",
"(C) Copyright Rosetta Commons Member Institutions.\n",
"Created in JHU by Sergey Lyskov and PyRosetta Team.\n",
"\n"
]
}
],
"source": [
"# This is needed for some builds\n",
"import rosetta\n",
"import pyrosetta\n",
"pyrosetta.init('-ignore_unrecognized_res T -ignore_waters T -preserve_header T -prevent_repacking T')"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"def tmalign( pose, ref_pose ):\n",
" \n",
" print 'Running tmalign on poses'\n",
" tm = rosetta.protocols.hybridization.TMalign()\n",
" tm.apply(pose, ref_pose)\n",
" longest = max(pose.total_residue()+1, ref_pose.total_residue()+1)\n",
" \n",
" print 'TMScore = %s ' %tm.TMscore(longest)\n",
" atommap = rosetta.core.id.AtomID_Map_core_id_AtomID_t()\n",
" rosetta.core.pose.initialize_atomid_map_AtomID( atommap, pose )\n",
" tm.alignment2AtomMap( pose, ref_pose, atommap )\n",
" aln_cutoff = rosetta.utility.vector1_double()\n",
" for i in [2.0,1.5,1.0,0.5]:\n",
" aln_cutoff.append(i)\n",
" min_coverage = .2\n",
" rosetta.protocols.hybridization.partial_align(pose,ref_pose, atommap, True, aln_cutoff, min_coverage)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false,
"scrolled": false
},
"outputs": [],
"source": [
"# Read in a pose and setup the pymol observer, you have to score it to get it into pymol\n",
"\n",
"p = pyrosetta.pose_from_file('2VBF_cleaned.pdb')\n",
"pm = pyrosetta.PyMolMover()\n",
"pm.keep_history(True)\n",
"pm.apply(p)\n",
"# sfxn = pyrosetta.get_fa_scorefxn()\n",
"# sfxn(p) "
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PDB file name: 2VBF_cleaned.pdb\n",
"Total residues:1082\n",
"Sequence: MYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIGNANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVEIVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYEIDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLENTTEQVILSKIEESLKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLPSFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMISLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDKQYEEFIPSSAPLSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLWGSIGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPICFIINNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRTENEFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNKMYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIGNANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVEIVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYEIDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLENTTEQVILSKIEESLKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLPSFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMISLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDKQYEEFIPSSAPLSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLWGSIGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPICFIINNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRTENEFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNK\n",
"Fold tree:\n",
"FOLD_TREE EDGE 1 181 -1 EDGE 1 182 1 EDGE 182 541 -1 EDGE 1 542 2 EDGE 542 722 -1 EDGE 1 723 3 EDGE 723 1082 -1 \n",
"vector1_unsigned_long[181, 541, 722]\n",
"MYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIGNANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVEIVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYEIDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLENTTEQVILSKIEESLKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLPSFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMISLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDKQYEEFIPSSAPLSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLWGSIGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPICFIINNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRTENEFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNK\n",
"vector1_unsigned_long[541]\n"
]
}
],
"source": [
"## Take a look at your protein and the wierd chain endings\n",
"print p\n",
"print p.conformation().chain_endings()\n",
"\n",
"# Fix the weird chain endings (so that later, we can create a nice foldtree)\n",
"p.update_pose_chains_from_pdb_chains()\n",
"print p.chain_sequence(1)\n",
"print p.conformation().chain_endings()\n",
"n_jumps = p.num_jump()\n",
"seq1 = p.chain_sequence(1)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [],
"source": [
"# Now, since the protein is in the right place, we just make a copy of the chain A\n",
"ChainAcopy = rosetta.core.pose.Pose(p,1,len(seq1))\n",
"ChainBcopy = rosetta.core.pose.Pose(p,len(seq1)+1,p.total_residue())"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"ChainA = rosetta.core.pose.Pose(p,1,len(seq1))\n",
"## Make third copy of chainA\n",
"## align copyChainA onto chainB\n",
"## Then turn the chain ID to Chain B on the copy\n",
"## then append chainb to chain A\n",
"## then dump pdb - then run make symm def file"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Running tmalign on poses\n",
"TMScore = 0.995005610329 \n"
]
}
],
"source": [
"tmalign(ChainAcopy,ChainBcopy)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"pm.apply(ChainAcopy)"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"for i in range(1,len(seq1)+1):\n",
" ChainAcopy.pdb_info().chain(i,'B')\n",
"ChainAcopy.pdb_info().obsolete(False)\n",
"ChainAcopy.dump_pdb('isthischainB.pdb')"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"rosetta.core.pose.append_pose_to_pose(ChainA,ChainAcopy)\n",
"ChainA.pdb_info().obsolete(False)\n",
"ChainA.dump_pdb('thismightworksymm.pdb')"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"rosetta.core.pose.append_subpose_to_pose(ChainA, ChainAcopy, 1, len(seq1), True)\n",
"ChainA.dump_pdb('thismightworksymm.pdb')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.13"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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