- modeller_usage - salilab.org

rigid.txt for PDBs with multiple subunits
by Robin Zhang 15 Dec '09

15 Dec '09

Hi, I'm trying to create a rigid.txt file for an antibody PDB file that contains multiple subunits (ie subunit A, subunit B, subunit C, and subunit D). However, the example in the ncmi_2008_files folder only contains a single subunit. Is there any way one can specify subunit as well as residue number in an rigid.txt file?

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Chain designation in completing a structure.
by Steve Seibold 15 Dec '09

15 Dec '09

Hello modeller I am attempting to "complete" a structure by placing in a loop and doing loop refinement. The problem I am having is setting up the "alignment.ali" correctly.I think? The protein has two chains, A and B. I am using the "alignment.ali" file shown below: Chain C starts with "1", Chain D starts with "2", and ends with 1505. So, Chain D has 1504 residues. The "python script" used for running Modeller is shown below the alignment.ali file. >P1;2PPB_CD structureX:2PPB_CD: 1 :C:1504:D:undefined:undefined:-1.00:-1.00 MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGE PPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTP DPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDES VFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKD EVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNS RPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIG LITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVS PEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVA IMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVK PGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRV YVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQR YISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLY DGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQ EMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKRKKEVR KVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVT KSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDE EYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFASILVVKARVYPFEDDVEVSTGDR VAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARR AKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPE IIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKL HQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQ AFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGL YYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVV TVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGF TFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEEN YPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTA DSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGR YLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMR TFHT-------DITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVK DGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRL LEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKE NVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEA* >P1;2PPB_CD_fill >Sequence::::::::: MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGE PPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTP DPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDES VFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKD EVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNS RPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIG LITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVS PEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVA IMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVK PGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRV YVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQR YISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLY DGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQ EMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKRKKEVR KVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVT KSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDE EYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFASILVVKARVYPFEDDVEVSTGDR VAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARR AKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPE IIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKL HQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQ AFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGL YYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVV TVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGF TFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEEN YPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTA DSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGR YLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMR TFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVK DGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRL LEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKE NVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEA* ---------------------------------------------------------------------------- The python script is: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('1244:D', '1250:D')) a = MyModel(env, alnfile = 'alignment.ali', knowns = '2PPB_CD', sequence = '2PPB_CD_fill') a.starting_model= 1 a.ending_model = 1 #a.loop.starting_model = 1 #a.loop.ending_model = 1 #a.loop.md_level = refine.fast a.make() ---------------------------------------------------------------------------- ---------------------------------------------------------------------- This procedure fails with the error printed to the screen: ........ ......... KeyError: 'No such residue: 1244:D' Am I designating the residue, chain correctly in the python script or is it the alignment.ali file that is causing the problem? I have tried several things and looked this up in the archives, but have not found anything directly related. I could have missed it..? Any help would be greatly appreciated. Thanks, Steve

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ab initio modelling with X-ray data
by leuven 15 Dec '09

15 Dec '09

Dear all: We have obtained a low resolution crystallography data for our protein, and we want to add it as restrain condition for ab initio modelling with MODELLER, just like the tutorial 5: Modelling with cyro-EM does, could it be done? And the data format of density map from crystallography is sca or mtz, while from EM it is mrc, how to fix it?

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No atoms were read form the specified input pdb file
by james09 pruza 14 Dec '09

14 Dec '09

Dear All, While running the model-single.py, I am getting the following error--- No atoms were read form the specified input pdb file since the starting residue no and/ or chain ID in Model_Segment <or the alignment file header> was not found; requested starting position residue no "0" chain "A" My model file starts with residue no 4. Please help. Thanks J

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distance restraints multi templates
by Armin Meier 14 Dec '09

14 Dec '09

Hi, we want to use Modeller for modeling a target with multiple templates. The distance restraints shall be replaced by our own ones. So far, we're replacing all lines in the restraints file of types 3 (gaussian) and 10 (spline) in combination with groups 9 (CACA), 10 (NO), 23 (SDCH-MNCH), 26 (SDCH-SDCH). Is there any source of information about the Modeller handling of distance restraints for multiple templates, i.e. which distance restraints are there and what is their mathematical form? Thanks for hints

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atom clashed
by leuven 10 Dec '09

10 Dec '09

Dear all: When I get the models from modeller, there are always some atom clash。How to solve this problem? Could modeller solve this by itself? I get models from "model-changeopt.py", and set a.md_level = refine.slow a.repeat_optimization = 50 Here is the results for the best model: Strongest energies for the vdWaals interactions _____________________________ _______________ 1 236 .GLU.N - 236 .GLU.CD 2.697 1.7143 2 318 .ASP.CG - 318 .ASP.C 2.844 1.7121 3 278 .ASP.CG - 278 .ASP.C 2.845 1.7029 4 99 .ASP.O - 101 .ASN.N 2.532 1.6450 5 143 .ARG.O - 161 .GLY.N 2.547 1.4700 6 250 .TYR.CG - 250 .TYR.C 2.885 1.3172 7 244 .ASP.O - 248 .ASP.N 2.563 1.3145 8 214 .ASP.CG - 214 .ASP.C 2.888 1.2951 9 411 .THR.O - 412 .LEU.C 2.710 1.2663 10 385 .ALA.O - 386 .ASP.C 2.713 1.2380 11 244 .ASP.N - 249 .ARG.O 2.578 1.1794 12 275 .SER.HA - 285 .ILE.O 2.185 1.1460 13 294 .ASP.O - 295 .GLY.C 2.725 1.1418 14 289 .TRP.CG - 289 .TRP.C 2.907 1.1394 15 276 .PHE.CG - 276 .PHE.C 2.914 1.0910 _____________________________________________________________________________ Strongest energies for the H-bonds interactions ____________________________________________ 1 344 .ASN.HD21- 344 .ASN.O 1.850 -1.5000 2 442 .ALA.O - 445 .SER.H 1.850 -1.5000 3 96 .GLY.O - 105 .VAL.H 1.850 -1.5000 4 397 .GLY.O - 399 .THR.H 1.850 -1.5000 5 230 .LEU.H - 235 .PHE.O 1.850 -1.5000 6 134 .ASP.OD2 - 164 .ARG.HH12 1.850 -1.5000 7 353 .ILE.O - 511 .ALA.H 1.850 -1.5000 8 398 .SER.HG - 398 .SER.O 1.849 -1.5000 9 106 .GLN.HE22- 142 .PHE.O 1.849 -1.5000 10 71 .PRO.O - 74 .LYS.H 1.849 -1.5000 11 206 .SER.HG - 208 .GLN.O 1.848 -1.4999 12 478 .ASP.O - 480 .SER.H 1.848 -1.4999 13 365 .VAL.O - 475 .SER.H 1.852 -1.4999 14 56 .LEU.O - 59 .TRP.HE1 1.848 -1.4999 15 177 .ASN.OD1 - 180 .LYS.H 1.852 -1.4999 _____________________________________________________________________________ Strongest energies for the Elect. interactions ____________________________________________ 1 31 .HIS.HE2 - 117 .PRO.O 1.872 -6.9175 2 50 .HIS.HE2 - 118 .TYR.O 1.940 -6.4947 3 406 .PRO.O - 513 .ASN.OD1 2.707 6.0365 4 348 .ASP.O - 513 .ASN.O 2.771 5.8644 5 294 .ASP.O - 295 .GLY.C 2.725 -5.8603 6 385 .ALA.O - 386 .ASP.C 2.713 -5.8427 7 340 .VAL.O - 524 .LEU.O 2.774 5.7495 8 411 .THR.O - 412 .LEU.C 2.710 -5.7430 9 326 .GLN.O - 488 .GLY.O 2.738 5.6908 10 9 .HIS.HE2 - 483 .GLU.OE2 1.871 -5.6896 11 134 .ASP.O - 135 .ILE.C 2.798 -5.6414 12 201 .ASP.O - 225 .VAL.O 2.878 5.5602 13 362 .GLN.OE1 - 530 .ASP.O 2.901 5.5484 14 386 .ASP.O - 387 .LEU.C 2.822 -5.5457 15 441 .ASP.CG - 441 .ASP.O 2.899 -5.4778 _____________________________________________________________________________ Non-bonded contributions _________________________ Normal pairs H-bonds : N.pairs= 14516 energy= -861. Elect. : N.pairs= 687078 energy= -0.402E+04 vdWaals : N.pairs= 699117 energy= -0.443E+04 1-4 pairs H-bonds : N.pairs= 5 energy= -0.137 Elect. : N.pairs= 21311 energy= 0.430E+04 vdWaals : N.pairs= 21306 energy= 288. Total H-bonds : N.pairs= 14521 energy= -861. Elect. : N.pairs= 708389 energy= 282. vdWaals : N.pairs= 720423 energy= -0.414E+04 Total non-bonded energy : -0.472E+04

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Modeling ligands in the binding site
by Qinghua Liao 10 Dec '09

10 Dec '09

Hi modeller users, Can modeller do ligand-steered modelling? And what is the difference between the ligand-steered method and the mothods from the on-line tutorial of Modeling ligands in the binding site? Are they the same method? Thanks very much! All the best, Qinghua fantasticqhl(a)yahoo.com

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Modeller on PPC64 with Linux - installation
by Wojciech Stach 09 Dec '09

09 Dec '09

Hello, Is there any way I could get Modeller installed on my machine: PPC64 with running Linux SLES 11? I browsed through all the downloadable files and it seems like none of them would be suitable to the abovementioned configuration... Any help will be greatly appreciated! Thanks, Wojciech

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Virtual conference Inbix '10: Cfp/Registrations starts!!
by Prash 08 Dec '09

08 Dec '09

Dear All, The first Indian virtual conference on Bioinformatics 2010 (Inbix'10): http://www.bioinformatics.org/wiki/Inbix10 Excellent opportunity to interact with leading scientists in the world in the area of Bioinformatics and Systems Biology! All for just Rs 500/- or 10 USD All the best Prash Prashanth Suravajhala C-DAC-Bioinformatics Group, Pune, India http://wiki.bioinformatics.org/prash I 'put a fullstop' as soon as I see myself complaining and blaming. These two habits destroy my inner power completely, because they show I am still expecting solutions and changes from others. Courtesy: Thought for Today

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Fw: Re: update
by leuven 06 Dec '09

06 Dec '09

I have made a new script and figured it out, the caculation speed is very fast now, thanks!

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