- modeller_usage - salilab.org

homology modelling vs protein threading
by Thomas Evangelidis 21 Dec '09

21 Dec '09

Dear modellers, I want to build models of ATP-binding domains with sequence identity ranging between 40% and 50%. In the FAQs it says that one needs 35-40% at least to build reliable models. However these models will be used for inhibitor design, therefore the accuracy of the structure prediction method will determine the outcome. Do you reckon the sequence similarity is enough to get a good model of the domain, or should I try other programs based on threading? Is there a way to compare the quality of the structures derived from these 2 different methodologies? I would greatly appreciate any advice. Thomas

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HIS and HSE
by Francesco Musiani 15 Dec '09

15 Dec '09

Hello, I would like to calculate an all atoms (including hydrogens) model of a metallo protein containing zinc. In particular, I would like to bind Zn2+ ion to ND1 atom of an histidine residues. I try to replace the residue "H" with "6" in the alignment (I referred to restyp.lib library found in modlib directory) but I obtain the following error in the log file. getpdf__392E> Your library requires all bins zero; nbinx: 5 can you help me? regards, Francesco -- Francesco Musiani -- Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna, Italy Phone: +39-051-2096236 - Fax: +39-051-2096203 E-mail: francesco.musiani(a)unibo.it

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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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