- modeller_usage - salilab.org

Chimeric alignment - residue numbers
by Larsson, Per (pl6n) 05 Jun '12

05 Jun '12

Hi! I am trying to build a model using the automodel class, based on two known structures where I want parts of the model to be based on structure A and parts on structure B. My alignment file looks like this: >P1;protein_a structureX:protein_a:1::238::::: aaaaaaaaaa---------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa--------------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-----------------------aaaaaaaaaaaaaaaa---------* >P1;protein_b structureX:protein_b:1::93::::: ----------bbbbbbbbb-----------------------------------bbbbbbbbbbbbbbbbbb-------------------------------------------bbbbbbbbbbbbbbbbbbbbbbbbbb-------------------------------------------------bbbbbbbbbbbbbbbbbbbbbbb----------------bbbbbbbb* >P1;chimera sequence:chimera:1::238::::: aaaaaaaaabbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaabbbbbbb* In my structure files, protein_a contains residues from 1-238. The residues in protein_b are a subset of the residues in protein_a, but I want restraints to be derived from protein_b for some parts of the final model. When running this in Modeller (v 9.10) i get the error read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 11) which I believe comes from the fact that since protein_a contains all residues, Modeller does not skip residues in the protein_a file, and a mismatch occurs. Do I need to remove residues from the structure in protein_a, or is there some way to tell Modeller to skip those residues when matching the sequence of residues in the structure file with the sequence of residues in the alignment file? Or alternatively tell Modeller to use restraints from only protein_b for parts of the model? Thanks /Per Larsosn

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Invitation to connect on LinkedIn
by Arvind Pal via LinkedIn 04 Jun '12

04 Jun '12

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signal peptide structure modeling
by Kwee Hong 31 May '12

31 May '12

Hi, I would like to model signal peptide structure. I would like to know is this possible with MODELLER? Or is there any relevant modeling server? Thanks, Joyce

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Re: [modeller_usage] PD: Re: optimization schedule
by M 31 May '12

31 May '12

Thank you very much, that was exacly what I wanted to know. Sorry for my poor description of those problems. > On 5/31/12 11:06 AM, M wrote: > > Thank you very much. One last question: how are the atoms (residues) > > chosen for individual CG step? For example if residue span range is > > 10, does it mean that only first residues are optimized? > > I don't know what you mean by "first residues" here. The schedule isn't > for picking which atoms are optimized (that is the job of the selection > - see automodel's select_atoms method - which by default is all atoms). > The schedule picks which *restraints* are optimized. If the span range > is 10, that means all atom-atom restraints that act on atoms in residues > at most 10 apart in sequence are optimized. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Re: [modeller_usage] PD: Re: optimization schedule
by M 31 May '12

31 May '12

Thank you very much. One last question: how are the atoms (residues) chosen for individual CG step? For example if residue span range is 10, does it mean that only first residues are optimized? > On 5/31/12 10:26 AM, M wrote: > > I was asking about the Conjugate gradients optimization > > initializations (each step of adding additional restraints), not > > about the steps of one CG process. > > Before the schedule is used in comparative modeling, schedule steps with > a range larger than the length of your sequence are removed, since they > are redundant; see > http://salilab.org/modeller/9.10/manual/node267.html > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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PD: Re: optimization schedule
by M 31 May '12

31 May '12

I don;t think I specified the problem well. This is a part of the output: # Conjugate gradients optimization # Step Current energy Av shift Mx shift Funcs Gradient 0 127763.69531 0.0000 0.0000 1 5.80191e+06 9 1023.20831 0.0001 0.0013 27 7958.03 # Conjugate gradients optimization # Step Current energy Av shift Mx shift Funcs Gradient 0 10585.82617 0.0000 0.0000 1 798323 10 3038.98022 0.0422 0.5213 21 44036.2 20 1562.34656 0.0573 0.4620 41 21124.6 30 952.08020 0.0387 0.3051 61 6975.25 40 718.60651 0.0190 0.1223 81 2768.92 50 613.78882 0.0165 0.1318 101 1072.04 60 558.44568 0.0191 0.1931 121 844.107 70 528.58771 0.0160 0.1610 142 623.547 80 505.49722 0.0071 0.0432 162 182.543 90 488.25266 0.0116 0.0833 182 371.858 100 472.90448 0.0159 0.2190 202 199.59 110 464.42642 0.0060 0.0553 222 123.018 120 459.06067 0.0065 0.0453 242 74.0072 127 456.91678 0.0008 0.0088 258 27.1187 # Conjugate gradients optimization # Step Current energy Av shift Mx shift Funcs Gradient 0 2565.44043 0.0000 0.0000 1 872.504 1 2564.90918 0.0005 0.0043 3 776.596 # Conjugate gradients optimization (...) I was asking about the Conjugate gradients optimization initializations (each step of adding additional restraints), not about the steps of one CG process. slow = schedule(4, [ step(CG, 2, mk_scale(default=0.01, nonbond=0.0)), step(CG, 4, mk_scale(default=0.10, nonbond=0.0)), step(CG, 6, mk_scale(default=0.50, nonbond=0.0)) ] + \ [ step(CG, rng, mk_scale(default=1.00, nonbond=0.0)) for rng in \ (8,10,14,18,20,24,30,25,40,45,50,55,60,70,80,90,100,120,140,160,200, 250,300,400,500) ] + \ [ step(CG, 600, mk_scale(default=1.00, nonbond=0.01)), step(CG, 800, mk_scale(default=1.00, nonbond=0.1)), step(CG, 1000, mk_scale(default=1.00, nonbond=0.5)), step(CG, 9999, physical.values(default=1.00)) ]) Number of steps from the script above is 32 (I understand, that those are the steps of each CG initializations), while CG initializations is smaller. I'm not asking about for example 9 steps of individual CG process from the top of the encolsed log fragment. Dnia 31-05-2012 o godz. 19:17 Modeller Caretaker <modeller-care(a)salilab.org> napisał(a): > On 5/31/12 9:53 AM, M wrote: > > While analysing the log file of the optimization proces (X.D00000001) > > I've discovered, that the number of steps is different than the > > number from the applied schedule. What is the cause? > > See http://salilab.org/modeller/9.10/manual/node258.html, in particular > the description of the min_atom_shift parameter. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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optimization schedule
by M 31 May '12

31 May '12

Hello, While analysing the log file of the optimization proces (X.D00000001) I've discovered, that the number of steps is different than the number from the applied schedule. What is the cause? The script I have used: from modeller import * from modeller.automodel import * env = environ() env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) log.level(output=1, notes=1, warnings=1, errors=1, memory=0) a = automodel(env, alnfile='alignment.pir', knowns='template', sequence='target', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 200 a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level = refine.slow a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() The autosched.slow schedule according to the file from the modeller folder consists of 32 CG steps, while the log file contains only 27 steps per iteration.

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short interatomic distances
by M 29 May '12

29 May '12

Hello, I have a problem concerning the step of evaluating my model. I'm using the whatif server (http://swift.cmbi.ru.nl/servers/html/index.html) Most of the scores are fine, but there are many abnormally short interatomic distances according to whatif. The problem doesn't result from the alignment. Is it possible that it is a result of different parametrization used by modeller (or by the implemented CHARMM force field)? Below is an enclosed example of the whatif log file concerning the short distances (two columns from the end with numbers are important: the first number in the table tells how much shorter that specific contact is than the acceptable limit, the second distance is the distance between the centres of the two atoms): 15 ILE ( 15-) A CG2 <-> 59 MET ( 59-) A SD 0.33 3.07 INTRA BF 179 MET ( 179-) A SD <-> 207 VAL ( 207-) B CG1 0.31 3.09 INTRA BL 19 THR ( 19-) A N <-> 252 LEU ( 252-) B CD2 0.28 2.82 INTRA BF 19 THR ( 19-) A CG2 <-> 55 ALA ( 55-) A CB 0.27 2.93 INTRA BF 154 VAL ( 154-) A CG2 <-> 156 LEU ( 156-) A CD2 0.27 2.93 INTRA BF 217 PHE ( 217-) B CE1 <-> 244 LEU ( 244-) B CD2 0.27 2.93 INTRA BF 105 TYR ( 105-) A CA <-> 186 ILE ( 186-) A CD1 0.27 2.93 INTRA BF 138 THR ( 138-) A CG2 <-> 139 LEU ( 139-) A CD1 0.26 2.94 INTRA BF 258 TYR ( 258-) B CB <-> 265 LEU ( 265-) B CD1 0.26 2.94 INTRA BF 19 THR ( 19-) A CB <-> 252 LEU ( 252-) B CD2 0.26 2.94 INTRA BF 65 THR ( 65-) A CG2 <-> 72 TRP ( 72-) A CE3 0.26 2.94 INTRA BF 179 MET ( 179-) A CE <-> 207 VAL ( 207-) B CG1 0.25 2.95 INTRA BL 239 VAL ( 239-) B CG1 <-> 243 PHE ( 243-) B CE2 0.25 2.95 INTRA BF 256 PHE ( 256-) B CE2 <-> 260 PHE ( 260-) B CZ 0.25 2.95 INTRA BF 220 LEU ( 220-) B CD1 <-> 235 ILE ( 235-) B CG1 0.25 2.95 INTRA BF 73 ILE ( 73-) A CD1 <-> 74 PHE ( 74-) A CD1 0.25 2.95 INTRA BF 33 VAL ( 33-) A CG1 <-> 35 LYS ( 35-) A CG 0.25 2.95 INTRA BL 25 LEU ( 25-) A CD2 <-> 269 TYR ( 269-) B CD1 0.25 2.95 INTRA BL 65 THR ( 65-) A CG2 <-> 72 TRP ( 72-) A CZ3 0.25 2.95 INTRA BF this is not a full list (fortunately other values are better, deviation from the acceptable value is small). Best regards, Mat

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breaking the chain
by M 29 May '12

29 May '12

Hi, I don't want to model one fragment of a protein. I want to achieve this by using the "\" sign in the alignment, but I'm not sure how the pir file should look after insertion of the "\" sign. Should it look like this: <P1 structureX: (...) ABCDEFGHJKLMNOPQRSTUVWXYZ* <P2 sequence: (...) ABCDEFGH\------QRSTUVWXYZ* or like this, with additional gap sign: <P1 structureX: (...) ABCDEFGHJKLMNOPQRSTUVWXYZ* <P2 sequence: (...) ABCDEFGH\-------QRSTUVWXYZ*

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modeling homodimer with hetero atoms
by NUTAN CHAUHAN 18 May '12

18 May '12

Dear all, I am trying to model a homodimer with heteroatoms from a homodimer template. when make homodimer without heteroatoms it goes fine but when i try to build homodimer with heteroatoms it doesn't run and shows some errors regarding alignment mistakes. My template protein consists of number of Waters, and other residues. All the htatms are given at the end of A and B chains and given the chain ids according to their chains they are attached with. I have removed all waters except three (1 is atached to A and 2 with B chain). So for now I have 7 and 8 hetatm on chain A and B respectively What should be the alignment look like? I am giving 7 dots at the end of A chain and 8 dots at the end of B chain as followes: >P1;2N0Y structureX:2N0Y:83 :A:687 :B: ferredoxin:Azotobacter vinelandii: 1.90: 0.19 -------------------------------------------PDMDTSF VGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE QGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTG QVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATS GRPGPVLVDLPKDVTAAILRNPIPTKTTLPSTSRAQDEFVMQSINKAADL INLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQED PKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRA AAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSK-----IFP VKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRH VIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKP ESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLF YEHRYSHTHQLN-----PDFIKLAEAMGLKGLRVKKQEELDAKLKEFVST KG-PVLLEVEVDKKVPVLPMVAGGSGLDEFINFDPEVERQQTELRHKRTG GKH/......./-------------------------------------------PDMDTSF VGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE QGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTG QVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATS GRPGPVLVDLPKDVTAAILRNPIPTKTTLPS-SRAQDEFVMQSINKAADL INLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQED PKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRA AAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSK-----IFP VKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRH VIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKP ESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLF YEHRYSHTHQLN-----PDFIKLAEAMGLKGLRVKKQEELDAKLKEFVST KG-PVLLEVEVDKKVPVLPMVAGGSGLDEFINFDPEVERQQTELRHKRTG GKH/......../* >P1;IRSH_NT sequence:IRSH_NT:44 :A:633 :B: ferredoxin:Peptococcus aerogenes: 2.00:-1.00 MSTNETSRAIEDHTTVSAPTKPHSPTFKPEPHSAANEPKHPAARPKHVAL QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHE QGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITG QVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAAS GRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQ-VREAAKL IAAARKPVLYVGGGVIR-GEATEQLRELAELTGIPVVTTLMARGAFPDSH RQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAK-- -------VIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG TIEMADWWAYLNGVRKTYPLSYGPQSDGS-LSPEYVIEKLGEIA---GPD AVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALP GTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLF YAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAI NDCPVVIDFIVGADAQVWPMVAAGTSNDEI-----QAARGIRPLFDDITE GHA/......./MSTNETSRAIEDHTTVSAPTKPHSPTFKPEPHSAANEPKHPAARPKHVAL QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHE QGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITG QVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAAS GRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQ-VREAAKL IAAARKPVLYVGGGVIR-GEATEQLRELAELTGIPVVTTLMARGAFPDSH RQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAK-- -------VIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG TIEMADWWAYLNGVRKTYPLSYGPQSDGS-LSPEYVIEKLGEIA---GPD AVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALP GTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLF YAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAI NDCPVVIDFIVGADAQVWPMVAAGTSNDEI-----QAARGIRPLFDDITE GHA/......../* Error that I am getting is: read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 607) Alignment .....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKH PDB ....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE Match ***** * * * Alignment residue type 13 (P, PRO) does not match pdb residue type 3 (D, ASP), for align code 1N0H (atom file 1N0H), pdb residue number "84", chain "B" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. I don't know why this error is appearing at the time of modeling with hetatm? Please help, Regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand ________________________________ From: "modeller_usage-request(a)salilab.org" <modeller_usage-request(a)salilab.org> To: modeller_usage(a)salilab.org Sent: Tuesday, 1 May 2012 4:15 AM Subject: modeller_usage Digest, Vol 11, Issue 51 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. Re: procheck problem. (Thomas Evangelidis) 2. Re: modelling with hetatms (Joel Tyndall) ---------------------------------------------------------------------- Message: 1 Date: Mon, 30 Apr 2012 14:05:39 +0300 From: Thomas Evangelidis <tevang3(a)gmail.com> To: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] procheck problem. Message-ID: <CAACvdx0LXyGWDhf0v+WGutoyXeEvpj7OD6pvNbJGXSjsgX5G3A(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Probably you overdid it with minimization. Try a smoother energy minimization scheme, e.g. 500-1000 steps. Also bare in mind that molecular mechanics force fields are not designed to produce crystallographic quality structures. I would rather use Rosetta (or PyRosetta) or http://www.yasara.org/minimizationserver.htm if I wanted to improve atom clashes, dihedral angles, secondary structure, etc. HTH, Thomas On 30 April 2012 13:47, vishal Nemaysh <vishal.bioinfotech(a)gmail.com> wrote: > Respected Sir, > > I have tried to minimize my pdb structure which is modeled by Modeller9v8. > i use the Discovery Studio plateform to minimize this pdb structure by > applying CHARMm force field and applying steepest descent and after that > conjugate gradient algorithm. > but the problem here is that the procheck result is not good as earlier. > such as in Ramachandran plot 87% amino acids are in favorable region before > minimization but after minimization only 55% amino acids are in favorable > range...so plz sir suggest me some solutions.... > > Thanking you, > > Your Sincerely > > -- > Vishal > Research Scholar, > University of Delhi, > North Campus > Delhi-110007 > M: 91+9650736653 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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