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Re: [modeller_usage] modeling homodimer with hetero atoms



Many thanx for quick response. This problem is solved..actually problem was in script..i just needed to put "env.io.water=True" to allow water as modeller was not reading water as hetatm and reading it as alignment mismatch with pdb. Its done now. thanx a lot.
One more query related to this is:
Is there any way to assign the residue numbers starting from 1 to each of the chain in the model? actually when I run modeller to model dimer, it assigns numbers to the residues of chain A and continues to chainB like if chain a get finished at 100 then it starts chain B from 101.

thnx in advance.
regards,
 
Nutan Chauhan
Research Scholar
Department of Biotechnology
BIT, Mesra
Ranchi-835215, Jharkhand


From: NUTAN CHAUHAN <>
To: "" <>
Sent: Friday, 18 May 2012 1:50 PM
Subject: modeling homodimer with hetero atoms

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
QGAGHMAEGYARASGKPGVVLVTS GPGATNVVTPMADAFADGIPMVVFTG
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
QGAGHAASGYAHVTGRVG VCMATSGPGATNLVTPLADAQMDSIPVVAITG
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: "" <>
To:
Sent: Tuesday, 1 May 2012 4:15 AM
Subject: modeller_usage Digest, Vol 11, Issue 51

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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 <" target="_blank" href="mailto:">>
To: " target="_blank" href="mailto:">
Subject: Re: [modeller_usage] procheck problem.
Message-ID:
    <CAACvdx0LXyGWDhf0v+" target="_blank" href="mailto:">>
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 <" target="_blank" href="mailto:">> 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
> " target="_blank" href="mailto:">
> 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: " target="_blank" href="mailto:">

          " target="_blank" href="mailto:">


website: https://sites.google.com/site/thomasevangelidishomepage/
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Message: 2
Date: Mon, 30 Apr 2012 22:34:17 +0000
From: Joel Tyndall <" target="_blank" href="mailto:">>
To: "Offord, Victoria" <" target="_blank" href="mailto:">>,
    "'" target="_blank" href="mailto:">'"    <" target="_blank" href="mailto:">>
Subject: Re: [modeller_usage] modelling with hetatms
Message-ID:
    <" target="_blank" href="mailto:">>
   
Content-Type: text/plain; charset="us-ascii"

Hi Tory,

On a quick glance, I am assuming you want to keep the sugars. You can specify which ones they are instead of using a generic "." E.g. Mannose is 2 Look in C:\Program Files (x86)\Modeller9.10\modlib\restyp_accelrys.lib for the full list.

Also there may some over-riding issue that excludes them as they are only in one template. Maybe you need to include a "." Before the dashes at the end other sequences e.g. SRW.----, this to me indicates a break of the chain and more residues "expected"

Hope this helps

J

From: " target="_blank" href="mailto:"> [mailto:" target="_blank" href="mailto:">] On Behalf Of Offord, Victoria
Sent: Friday, 27 April 2012 1:55 a.m.
To: '" target="_blank" href="mailto:">'
Subject: [modeller_usage] modelling with hetatms

Dear Modeller,

I have been trying to include some hetatms in my models but so far all that seems to appear apart from the main chain is a few characters at the end of the modelled sequence.  I know that there must be something obvious that I am doing wrong but cannot for the life of me work out what it is!

I have modified the PDBs 2Z7X, 2Z80, 2Z82 and 3A79 to include only the chain of interest (using PyMOL) and only in 2Z7X have I kept the HETATMs of interest.  I have copied in my script and alignment below.

Any help that can be offered would be so very much appreciated!

Best wishes,

Tory

from modeller import *
from modeller.automodel import *

log.verbose()
env = environ()
env.io.atom_files_directory = ['/home/tory/data/bTLR2_april12/PDBs/']
env.io.hetatm = True

a = automodel(env,
                                                                alnfile='../modeller_alignment_with_glyc_pir_format.ali',
                knowns=('2Z7XchainA','2Z82chainA','3A7BchainA','2Z80chainB'), sequence='btau-tlr2',
                assess_methods=(assess.DOPE, assess.normalized_dope, assess.DOPEHR, assess.GA341))
a.starting_model = 1
a.ending_model = 50

# Very thorough VTFM optimization:
a.library_schedule = autosched.slow
a.max_var_iterations = 300

# Thorough MD optimization:
a.md_level = refine.slow

# Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6
a.repeat_optimization = 5
a.max_molpdf = 1e6

a.make()


>P1;2Z82chainA
structureX:2Z82chainA::A:548:A:TLR2:mus musculus:2.60:0.22
-SLSCDASGVCDGRSRSFTSIPSGLTAAMKSLDLSFNKITYIGHGDLRACANLQVLILKS
SRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLF
PNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTL
HLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDES
FNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLF
YDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGA
WPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSS
TGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMK
ISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW----*
>P1;3A7BchainA
structureX:3A7BchainA::A::A:TLR2:mus musculus:2.53:0.24
ESLSCDASGVCDGRSRSFTSIPSGLTAAMKSLDLSFNKITYIGHGDLRACANLQVLILKS
SRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLF
PNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTL
HLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDES
FNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLF
YDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGA
WPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSS
TGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMK
IASNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW----*
>P1;2Z7XchainA
structureX:2Z7XchainA:27:A:::TLR2:homo sapiens:2.10:0.24
-SLSCDRNGICKGSSGSLNSIPSGLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTS
NGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLF
SHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLIL
HMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDES
LFQVMKLLNQISGLLELEFDDCTLNGVGNFRASDNDRVIDPGKVETLTIRRLHIPRFYLF
YDLSTLYSLTERVKRITVENSKVFLVPCLLSQHLKSLEYLDLSENLMVEEYLKNSACEDA
WPSLQTLILRQNHLASLEKTGETLLTLKNLTNIDISKNSFHSMPETCQWPEKMKYLNLSS
TRIHSVTGCIPKTLEILDVSNNNLNLFSLNLPQLKELYISRNKLMTLPDASLLPMLLVLK
ISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW....*
>P1;2Z80chainB
structureX:2Z80chainB::B::B:TLR2:homo sapiens:1.80:0.22
-SLSCDRNGICKGSSGSLNSIPSGLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTS
NGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLF
SHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLIL
HMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFS-------NSLIKKFTFRNVKITDES
LFQVMKLLNQISG-----------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----------------------------------------------*

>P1;btau-tlr2
sequence:btau-tlr2:::::TLR2:bovine AAL16722|AF368419:2.00:-1.00
SSLSCDPTGVCDGHSRSLNSIPSGLTAGVKSLDLSNNDITYVGNRDLQRCVNLKTLRLGA
NEIHTVEEDSFFHLRNLEYLDLSYNRLSNLSSSWFRSLYVLKFLNLLGNLYKTLGETSLF
SHLPNLRTLKVGNSNSFTEIHEKDFTGLTFLEELEISAQNLQIYVPKSLKSIQNISHLIL
HLKQPILLVDILVDIVSSLDCFELRDTNLHTFHFSEASISEMSTSVKKLIFRNVQFTDES
FVEVVKLFNYVSGILEVEFDDCTHDGIGDFRALSLDRIRHLGNVETLTIRKLHIPQFFLF
HDLSSIYPLTGRVKRVTIENSKVFLVPCLLSQHLKSLEYLDLSENLMSEETLKNSACKDA
WPFLQTLVLRQNRLKSLEKTGELLLTLENLNNLDISKNNFLSMPETCQWPGKMKQLNLSS
TRIHSLTQCLPQTLEILDVSNNNLDSFSLILPQLKELYISRNKLKTLPDASFLPVLSVMR
ISRNIINTFSKEQLDSFQQLKTLEAGGNNFICSCDFLSFTQGQ....*
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