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,

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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 <tevang3@gmail.com>
To: modeller_usage@salilab.org
Subject: Re: [modeller_usage] procheck problem.
Message-ID:
    <CAACvdx0LXyGWDhf0v+WGutoyXeEvpj7OD6pvNbJGXSjsgX5G3A@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@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@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@bioacademy.gr

          tevang3@gmail.com


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 <joel.tyndall@otago.ac.nz>
To: "Offord, Victoria" <vofford@rvc.ac.uk>,
    "'modeller_usage@salilab.org'"    <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] modelling with hetatms
Message-ID:
    <0DDD35E86921D947AFE9571F16DA7D6BB9F460@ITS-EXM-P05.registry.otago.ac.nz>
   
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: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Offord, Victoria
Sent: Friday, 27 April 2012 1:55 a.m.
To: 'modeller_usage@salilab.org'
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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