- modeller_usage - salilab.org

changing the seed
by Amanda Moraes 18 Mar '09

18 Mar '09

Hi! My name is Amanda and I`ve read that changing modeller seed helps to achieve a better model. In my top file, where can I put the new comand? And how to write it? I know that the number must be negative. Sorry for the stupid question. Thank you in advance! Amanda Maia INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'novo_alinhamento.ali' # alignment filename SET KNOWNS = '1MDY' '1NKP' '2QL2' '1HLO' # codes of the templates SET SEQUENCE = 'twist1' # code of the target SET STARTING_MODEL = 1 SET ENDING_MODEL = 100 CALL ROUTINE = 'model' # do homology modelling Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Modelling of a copper binding cluster
by Stephen.Hearnshaw＠uea.ac.uk 12 Mar '09

12 Mar '09

Dear all, I require some guidance with a modelling problem I am having. I am attempting to model a short 11 residue sequence around a template taken from the small molecule database: ATOM 1 SG CYS A 1 4.774 5.927 9.587 1.00 0.00 ATOM 2 CB CYS A 1 4.175 7.673 9.917 1.00 0.00 ATOM 3 SG CYS A 2 5.091 3.544 6.534 1.00 0.00 ATOM 4 CB CYS A 2 6.560 3.252 7.614 1.00 0.00 ATOM 5 SG CYS A 3 1.160 3.172 6.513 1.00 0.00 ATOM 6 CB CYS A 3 0.028 2.178 7.542 1.00 0.00 ATOM 7 SG CYS A 4 0.936 5.818 9.617 1.00 0.00 ATOM 8 CB CYS A 4 -0.419 4.795 10.238 1.00 0.00 ATOM 9 SG CYS A 5 2.942 2.405 9.819 1.00 0.00 ATOM 10 CB CYS A 5 4.547 1.918 10.664 1.00 0.00 ATOM 11 SG CYS A 6 2.713 6.590 6.171 1.00 0.00 ATOM 12 CB CYS A 6 2.800 5.754 4.601 1.00 0.00 HETATM 13 CU CU1 A 7 2.896 4.649 9.731 1.00 0.00 HETATM 14 CU CU1 A 8 4.201 5.454 7.463 1.00 0.00 HETATM 15 CU CU1 A 9 3.182 2.965 7.621 1.00 0.00 HETATM 16 CU CU1 A 10 1.497 5.188 7.518 1.00 0.00 END I require the first 4 CYS residues of the template structure to align with 4 CYS residues from my query sequence (as shown in the following alignment), and for the orientation of these residues around the copper cluster to be maintained >P1;TemplateTest Structure:templatetest:1:A:10: : : : : C-C-----C-CCC....* >P1;Ace1 Sequence:Ace1: : : : : : : : CRCDEGEPCKC--....* I have performed an unrestrained alignment that produced a model, but was unable to keep the CYS residues in the correct orientation and moved the polypeptide 80A away from the copper cluster! Attempts to restrain the system, by putting distance restraints between the SG atoms of the CYS residues and coppers have been unsuccessful. The following is an example of the commands I have been trying as a distance restraint. rsr.add(forms.upper_bound(group=physical.xy_distance, feature=features.distance(at['CU:7:A'], at['SG:1']), mean=2.28, stdev=0.01)) Any guidance that could be given on this problem would be much appreciated! Regards Stephen Hearnshaw

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import pylab error
by vamsi 09 Mar '09

09 Mar '09

Dear all, I have encountered a problem when i try to plot dope values as shown in the tutorial using plot_profile script, but giving import pylab error. As suggested in the tutorial matplotlib package has been installed and i am not sure how to specify the path to pylab, which is located matplotlab package. I hope some one can help me. to solve this problem and suggest how exactly to use gnuplot for same purpose Thank you with regards, vamsi

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Problem applying two different restrictions ...(solved)
by Sergio Garay 06 Mar '09

06 Mar '09

Dear Dr. Arvind and Dr. Webb Thank you very much for your help. The problem as you point out was the lacking of the cystein's chain identification. Below I paste the corrected script (in case other people look up this kind of errors in the list): # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class MyModel(automodel): def special_patches(self, aln): # A disulfide between residues 345 and 668: self.patch(residue_type='DISU', residues=(self.residues['*345:A'*], self.residues['*668:A'*])) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' # Read in HETATM records from template PDBs env.io.hetatm = True a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('2ioaB_amidase', '2vobB', '2ioaB_sinthetase'), # codes of the templates sequence = 'tcruzi') # code of the target a.starting_model= 3 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Problem applying two different restrictions....
by Sergio Garay 05 Mar '09

05 Mar '09

Dear all My name is Sergio Garay and I am pretty new using modeller so it is probable that my questions can be "a little" silly. I am trying to build a model with two kind of restrictions (using a multiple templates alignment): a disulphide bridge and the position of ligands. I was able to obtain (following your tutorial) models with each restriction applied in a separate way. The problem appear (errors) when I try to combine both restriction at the same time. I am using mod9v6, and I follow the examples of that version. Is there any problem in my py script? Any help will be appreciated. *Below I've pasted the python script that I used*: # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class MyModel(automodel): def special_patches(self, aln): # A disulfide between residues 345 and 668: self.patch(residue_type='DISU', residues=(self.residues['345'], self.residues['668'])) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' # Read in HETATM records from template PDBs env.io.hetatm = True a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('2ioaB_amidase', '2vobB', '2ioaB_sinthetase'), # codes of the templates sequence = 'tcruzi') # code of the target a.starting_model= 3 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling *The error in the terminal: * Traceback (most recent call last): File "model-mixed.py", line 30, in ? a.make() # do the actual homology modeling File "/usr/lib/modeller9v6/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib/modeller9v6/modlib/modeller/automodel/automodel.py", line 427, in homcsr self.make_initial_model(aln) File "/usr/lib/modeller9v6/modlib/modeller/automodel/automodel.py", line 441, in make_initial_model self.generate_method(self, aln) File "/usr/lib/modeller9v6/modlib/modeller/automodel/generate.py", line 25, in transfer_xyz mdl.create_topology(aln) File "/usr/lib/modeller9v6/modlib/modeller/automodel/automodel.py", line 659, in create_topology self.special_patches(aln) File "model-mixed.py", line 10, in special_patches self.patch(residue_type='DISU', residues=(self.residues['345'], File "/usr/lib/modeller9v6/modlib/modeller/coordinates.py", line 226, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v6/modlib/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v6/modlib/modeller/coordinates.py", line 283, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 345' *The log file write by Modeller:* MODELLER 9v6, 2009/01/30, r6593 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2009 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux leichmania.unl.edu.ar2.6.26.8-57.fc8 x86_64 Date and time of compilation : 2009/01/30 23:00:55 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2009/03/05 07:20:23 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v6}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v6}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v6}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 3.131 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v6}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v6}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v6}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v6}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v6}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v6}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v6}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v6}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 io_data____W> Setting io.atom_files_directory to a colon-delimited string is deprecated, as it is not robust on Windows systems. Set it to a list of directories instead. For example: env.io.atom_files_directory = ['./', '../atom_files'] openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3303901 3226.466 3.151 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3305351 3227.882 3.152 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3308251 3230.714 3.155 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3314051 3236.378 3.161 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3325651 3247.706 3.172 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3554183 3470.882 3.390 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3554211 3470.909 3.390 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3554239 3470.937 3.390 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3554267 3470.964 3.390 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3554295 3470.991 3.390 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3555003 3471.683 3.390 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3557363 3473.987 3.393 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3559015 3475.601 3.394 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3561899 3478.417 3.397 read_al_374_> Non-standard residue type,position,sequence: . 739 3 read_al_374_> Non-standard residue type,position,sequence: . 740 3 read_al_374_> Non-standard residue type,position,sequence: . 741 3 read_al_374_> Non-standard residue type,position,sequence: . 739 4 read_al_374_> Non-standard residue type,position,sequence: . 740 4 read_al_374_> Non-standard residue type,position,sequence: . 741 4 Read the alignment from file : alignment.ali Total number of alignment positions: 741 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ioaB_ami 178 1 2ioaB_amida 2 2vobB 591 1 2vobB 3 2ioaB_sin 414 2 2ioaB_sinth 4 tcruzi 722 2 tcruzi check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./2ioaB_amidase.pdb Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3665465 3579.556 3.496 openf___224_> Open ./2vobB.pdb Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4011534 3917.514 3.826 openf___224_> Open ./2ioaB_sinthetase.pdb Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4253508 4153.816 4.056 replace_706W> BLK ('.') residue type in alignment will force 'automodel' model building to treat residue type MG as a rigid body, even though topology information appears to be at least partially available. To treat this residue flexibly instead, use 1-letter code ' $' in the alignment. replace_706W> BLK ('.') residue type in alignment will force 'automodel' model building to treat residue type MG as a rigid body, even though topology information appears to be at least partially available. To treat this residue flexibly instead, use 1-letter code ' $' in the alignment. replace_706W> BLK ('.') residue type in alignment will force 'automodel' model building to treat residue type ADP as a rigid body, even though topology information appears to be at least partially available. To treat this residue flexibly instead, use 1-letter code ' &' in the alignment. fndatmi_285W> Only 411 residues out of 414 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- drmsq1__W> n<2 drmsq3__W> n<2 248 2 3 215 204 P I 7.832 249 2 3 216 205 P A 6.141 371 2 3 335 324 N R 6.155 405 2 3 368 356 G G 6.617 407 2 3 370 357 D N 6.545 508 2 3 466 451 D I 6.965 509 2 3 467 452 Y R 6.999 524 2 3 477 464 N I 10.068 530 2 3 482 469 P P 7.125 588 2 3 539 525 E L 6.179 592 2 3 543 529 H G 6.116 596 2 3 547 533 K K 7.078 601 2 3 578 536 R A 15.389 667 2 3 579 565 N N 6.052 707 2 3 617 605 S I 6.995 END OF TABLE fndatmi_285W> Only 411 residues out of 414 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- 45 1 31 43 R I 15.730 288 2 250 265 G F 19.941 513 3 454 459 A W 9.670 600 2 551 578 G R 11.251 721 2 632 637 R Q 14.815 END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${MODINSTALL9v6}/modlib/models.lib openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 5202292 5080.363 4.961 openf___224_> Open ${LIB}/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5315018 5190.447 5.069 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5876166 5738.443 5.604 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5963014 5823.256 5.687 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 18 719 atom names : C +N atom indices : 5706 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 18 719 atom names : C CA +N O atom indices : 5706 5702 0 5707 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 719 5707 5854 0 0 2501 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6209366 6063.834 5.922 patch_______> segment topology patched using RTF: 1 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 1 719 5707 5854 7949 9437 2501 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6484142 6332.170 6.184 patch_______> segment topology patched using RTF: 719 ; VAL ; CTER segments residues atoms bonds angles dihedrals impropers: 1 719 5708 5855 7951 9439 2502 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 719 5708 5855 7951 9439 2502 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 6484170 6332.197 6.184 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6484641 6332.657 6.184 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6486699 6334.667 6.186 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 722 5737 5855 7951 9439 2502 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 722 5737 5855 7951 9439 2502 fndatmi_285W> Only 411 residues out of 414 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) *The alignmet used: * >P1; 2ioaB_amidase structureX:2ioaB_amidase:12:B:200:B:::-1.00:-1.00 -------------------FGTLLGYAPGGVAIYSSD---Y---SV-------------- FRSYIDDEYMGHKWQCVEFARRFLFLNYGVVFTDVGMAWEIFSLRFLREVVND-NILPLQ AFPNGSPRAPVAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWT RELEMVVEN-GCYTLKD-TFD-D-TTILGWMIQTEDTEYSLP------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------/---* >P1; 2vobB structureX:2vobB:5:B:652:B:::-1.00:-1.00 -----QRASVSFNKPGHIPFGAVQGYAPGGVPAYSNKHDHYFSG---------------- ERNIEDNIFFGFKYQCVEFARRWLLVRKGLLLPDVNWACHIFQLKEVRDAATT-ESFAVL QVRNGTTTKPEADALLVYPSTDAN-PVGHVGTITEVGDDYVCVADQNYRFHKWE--SSCA YKLKLDHRD-GIWTIIDDIDADEIEIPLGWLTFP--------GRANRPEGAPPVALHPSL HFKE---PP--KPYLLRRNF-LPW--------LDMNNPAERLFVEEFG----------VS YYESNHEFHLRCVAYGTQLHAIFMEATAQVIESDEKLRLFAIPEEFWPRIRHSWKYQQ-T YISGRFDFAFNNETGEVKCFEYNADSASTLLECGLIQQKWAESV-GLDDTRGSGFAVERN LKMAWANSG------ATGRVHFCVDEEREEQYTALYCMQAAEAVGLEGKLCILFDEFRF- DDNGHVVDSDGVRVRNVWKTWMWESAITDYYAAR-----EERGEN-WKPSPK-DKVRLCD LLLGDDWEILYFEPMWKVIPSNKAILPMIYHNHPEHPAILKAEYELTDELRKHGYAKKPI VR---------------------------------------------------------- -------NMIYQQLFELKKQDDYYAIIGGWMIGDAFSGTGIREDK--S-----PFAAVRI -KPHPVTLKDIDKMAEDE-/---* >P1; 2ioaB_sinthetase structureX:2ioaB_sinthetase:201:B:621:B:::-1.00:-1.00 ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----QPEIAGELLKISGARLEN--KGQFDGKWLDEKDPLQNAYVQAN--GQVINQDPYHY YTITESAEQELIKATNELHLMYLHATDKVLKDDNLLALFDIPKILWPRLRLSWQRRRHHM ITGRMDFCMDER--GLKVYEYNADSASCHTEAGLILERWAEQGYKG-NGFNPAEGLINEL AGAWKHSRA------RPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRGLDELGW-- G--QLIDGEGRLVNCVWKTWAWETAFDQIRE--VFAAVP-----IR-TGHPQNEVRLIDV LLR--PEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLLDTDFTVNDELVKTGYAVKPI- -AGRCGSNIDLVSHH-------------------------------------EEVLDKTS GKFAEQKNIYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGDESLVIKKESDIEPLIVV K------------------/...* >P1; tcruzi sequence:tcruzi:::::::0.00:0.00 MENTDKQRGVHASETEHVSFGGVIGVTDCGVPVFSNGEKKFFSERISFAPDCKRVEAAAP TTVIGTHDTLGYKWLCLEFARRYLLMTKGVWLASVPTAEDIWEIDEIVTSVPIGTPVPVE REKHGDTTSMPSVGDLLVWSRTEDSPYGHLAVVTHVSDNGVCVAEQNYEFKRWQEGKNYS RRFDCEKREDGVTVFVGETHLLGWVIIKAPPYDFSLGDLPDKYRHIIGPGHIVRRHLEKD VLLPWLNPSQRCDFFLKRSLTVG--------GYMGEDAVAEAHSVPDG------------ FYMMDYDMWCRFRFATKNLHAVAVEATRLILNSRDSEALLVQYFGLPKELHLQLRRSFET IPSMCGRFDFGYDGKEIIMLAYNCDSSAAMLECGDTQEKFARHYGVELGTSTGSFLYSRI ANYFNCLIQNEFLCPHHKIVHFMIDDDDEERYTALYVMNAAESAGFRTKLCVKLSGFRFG STTGEVDRDASPTERRSVVDLENEEVLLVWKTWAWDTVLRQYVEQRTQQGHGVSTKPTLS DILLNEHIRVLEPLWKAVTGSKAILPFMYAAAPHHSNMVPASFYRTKEIISAPYLTKPVN GRSGKSMTMYDTGEDPEAVAAAPHTAAAPVLGRSISAVLFDDAPAGTYRVPFDNIQENLT ERLFDSVVVYQSRVFLTRYEKKYSPIFCGWNVGGEFGGVIVREENFNNTKLSSLVIPSRV VRQHIPLHAMQESTTSGEV/...* -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Combining steps in Basic and Advanced Tutorial ?
by Ashika Umanga Umagiliya 04 Mar '09

04 Mar '09

Dear Modeller caretaker, I follow the steps 1 and 2 in the 'Basic tutorial'. Then using the generated 'build_profile.prf' during step 2; I select upto maximum 5 templates with lowest e-value. Then I proceed with steps on 'Advanced tutorial'.ie in 'salign.py', I use above selected templates for modelling.. How accurate is my procedure? Best Regards, Umanga -- アシカウマンガウマギリヤ㈱国際バイオインフォマティクス研究所（BiGG) 〒140-0001 東京都品川区北品川3-6-9 アンドウビル8F TEL:03-6679-8763 FAX:03-6679-8764

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Completing missing residues
by Lee Soin 04 Mar '09

04 Mar '09

Hello, all! I have a PDB file that has several consecutive residues missing. Can MODELLER help to complete them? And how? Thanks! -- SUN Li Department of Physics Nanjing University, China

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Modeller and DNA-protein complexes.
by Chaix Denis 03 Mar '09

03 Mar '09

Dear ALL I want to use have Modeller, DNA-protein complexes. I have a structure of a protein:DNA as a template and the sequence of an unknown dna binding protein structure I have already made the alignement Could modeller model the unknown protein and the unknown DNA structure? What is the good protocol to obtain a good model Best, Denis -- CHAIX Denis Centre de Biochimie Structurale INSERM U554/CNRS 5048 29 rue de Navacelles F-34090 Montpellier, France Tel: 33 4 67 41 77 21 Fax: 33 4 67 41 79 13 e-mail:Denis.chaix@cbs.cnrs.fr http://www.cbs.cnrs.fr

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Histidine protonation state with allhmodel
by Jean Didier Pie Marechal 03 Mar '09

03 Mar '09

Dear All, I am building a model with a specific zinc coordination sphere. I decided to use a full atom run and this actually improved the overall quality of the models. I have a problem though. In the structure, the zinc is chelated by several histidines some by delta others by epsilon chelating modes. However, the resulting models are always with the same protonation state (epsilon). This leads to undesired clashes. How can I stipulate modeller to use a given protonation state with the charmm force field. Should I use the charmm residue code in the initial pdb? Or should I define this in the python script. Thanks for any help Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: modeller_usage-request(a)salilab.org Data: Divendres, Febrer 20, 2009 4:02 pm Assumpte: modeller_usage Digest, Vol 8, Issue 12 > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Academic and Commercial (salam pradeep) > 2. Re: Academic and Commercial (Modeller Caretaker) > 3. Using modeller with a web form: how topass the provided key > to modeller? (St?phane T?letch?a) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 18 Feb 2009 15:12:48 +0530 > From: salam pradeep <salampradeep(a)gmail.com> > Subject: [modeller_usage] Academic and Commercial > To: modeller_usage(a)salilab.org > Message-ID: > <901340f20902180142w8dd888nc1b6e9a2be8ce262(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Is there any variation in the models generated by the Academic > version and > the Commercial version of Modeller. > Some people say that the Modeller Academic version is not so > accurate in > generating the 3D models. > How far is it true. >

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loop modeling based on a template
by Marco Neves 03 Mar '09

03 Mar '09

Hi, I have two pdb files of the same protein in complex with different ligands. PDB1 has all residues. PDB2 misses a small loop. Is it possible to model the missing loop of PDB2 based on the corresponding residues of PDB1 while keeping all other residues in the exact same positions? Which functions should be used? Thank you very much! marco neves

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