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Today's Topics:

   1. Re: loop modeling limits (Modeller Caretaker)
   2. Re: specify sequence ranges for salign/align2d
      (Modeller Caretaker)
   3. ERROR: No alignment (Joydeep)


----------------------------------------------------------------------

Message: 1
Date: Wed, 10 May 2006 12:44:28 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
Subject: Re: [modeller_usage] loop modeling limits
To: lorix <Loris.Moretti@pharm.unige.ch>
Cc: modeller_usage@salilab.org
Message-ID: <4462429C.6050205@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

lorix wrote:
> I would like to build part of a protein which is missing from the PDB file.
> It is a very long loop (72 residues) and I am not sure if the task is
> beyond Modeller skills.

Any loop longer than 12 residues or so is going to be essentially
impossible to model with this protocol - the conformational space is
just too large. You should try to find other templates with reasonable
sequence identity to cover at least part of this long loop.

    Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

Message: 2
Date: Wed, 10 May 2006 12:52:11 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
Subject: Re: [modeller_usage] specify sequence ranges for
    salign/align2d
To: Douglas Kojetin <douglas.kojetin@gmail.com>
Cc: modeller_usage@salilab.org
Message-ID: <4462446B.7070505@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Douglas Kojetin wrote:
> WIth reference to Tutorial 2 (Advanced Modeling):
>
> http://salilab.org/modeller/tutorial/advanced.html
>
> Is it possible to:
>
> (1) specify the sequence number ranges for the templates to be used in
> the structural alignment within 'salign.py'?
>
> or
>
> (2) specify the sequence number ranges for the template or target to be
> used in the sequence alignment within the script 'align2d_mult.py'?

Of course - both of these are straightforward.

For (1), just specify model_segment when you read in the model. The
example you mention reads a whole chain for each PDB, but you can read
whatever you like, e.g.

aln = alignment(env)
mdl = model(env, file='foo.pdb', model_segment=('1:', '34:'))
aln.append_model(mdl, atom_files='foo', align_codes='foo')
mdl = model(env, file='bar.pdb', model_segment=('3:A', '95:B'))
aln.append_model(mdl, atom_files='bar', align_codes='bar')

and so on... This makes an alignment of residues 1-34 from 'foo.pdb'
against residues 3:A to 95:B from 'bar.pdb'.

For (2), you can give the residue range in the alignment file header.
See http://salilab.org/modeller/manual/node176.html. The example there
reads residues 1-106 for the 5fd1 structure, and 1-54 for the 1fdx sequence.

    Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

Message: 3
Date: Thu, 11 May 2006 10:23:06 -0400 (EDT)
From: "Joydeep" <joy_alwayslate@excite.com>
Subject: [modeller_usage] ERROR: No alignment
To: modeller_usage@salilab.org
Message-ID: <20060511142306.928DC99DF4@xprdmxin.myway.com>
Content-Type: text/plain; charset="us-ascii"

Hi,
I'm trying to model a large protein(763 amino acids) with a distant template obtained from mGenThreader...but when i run the model.py command (as shown in tutorial), i get the following:
--------------------------------------------------------------------
Type 'mod8v2' to run Modeller.

C:\Modeller>mod8v2 c:\Mitra\Project_Experiments\the_align\theAlignment.top
'import site' failed; use -v for traceback

C:\Modeller>mod8v2 c:\Mitra\Project_Experiments\the_align\model.py
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "c:\Mitra\Project_Experiments\the_align\model.py", line 9, in ?
    a.make()
  File "C:\Modeller\modlib\modeller\automodel\automodel.py", line 100, in make
    self.homcsr(exit_stage)
  File "C:\Modeller\modlib\modeller\automodel\automodel.py", line 331, in homcsr

    aln.check()
  File "C:\Modeller\modlib\modeller\alignment.py", line 153, in check
    io=io.modpt, libs=libs.modpt, **vars)
  File "C:\Modeller\modlib\modeller\util\top.py", line 37, in check_alignment
    return _modeller.check_alignment(aln, io, libs, *args)
_modeller.error: check_a_335E> No alignment.

C:\Modeller>
---------------------------------------------------------------------
I checked the alignment file, it seems okay to me...so i can't figure out what's going wrong. Can someone please tell me what could possibly be wrong with the alignment?

Thanks in advance
Joy




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-------------- next part --------------
>P1; 2CAS
structure:2CAS:37::584:.::::
----------------------------------------GVGISTGTFNNQTEFKFLENGWVEITANSS
RLVHLNMPESENYRRVVVNN----------------MDKTAVNGNMALDDIHAQIVTPWSLVDANAWGVW
FNPGDWQLIVNTMSELHLVSFEQEIFNVVLKTVSESATQPPTKVYNNDLTASLMVALDSNNTMPFTPAAM
RSETLG-------FYP----------------------------WKPTIPTPWRYYFQWDRTLIPSHTG-
TSGTPTNIYHGTDPDD----VQFYTIENSVPVHLLRTGDEFATGTFFFDCKPCR------------LTHT
WQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQ-------MGNTNYITEATIMRPAEVGYSAP
YYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFGRQHGQKTTTTGETPERFTYIAHQDTGRYPE
------GDWIQNINFNLPVTNDNVLLPTDPIGGKTG--------------INYTNIFNTYGPLTALNNVP
P------------------------VYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVKVAPNLT
NEYDPDAS--ANMSRIVTYSDFWWKGKLVFKAKLRASHTWN---PIQQMSINVDN----------QFNYV
PSNIGGMK----IVYEKSQLAPRKLY--------------------------------------*

>P1;SATB1
sequence:SATB1:.:.:.:.::::
MDHLNEATQGKEHSEMSNNVSDPKGPPAKIARLEQNGSPLGRGRLGSTGAKMQGVPLKHSGHLMKTNLRK
GTMLPVFCVVEHYENAIE YDCKEEHAEFVLVRKDMLFNQLIEMALLSLGYSHSSAAQAKGLIQVGKWNPV
PLSYVTDAPDATVADMLQDVYHVVTLKIQLHSCPKLEDLPPEQWSHTTVRNALKDLLKDMNQSSLAKECP
LSQSMISSIVNSTYYANVSAAKCQEFGRWYKHFKKTKDMMVEMDSLSELSQQGANHVNFGQQPVPGNTAE
QPPSPAQLSHGSQPSVRTPLPNLHPGLVSTPISPQLVNQQLVMAQLLNQQYAVNRLLAQQSLNQQYLNHP
PPVSRSMNKPLEQQVSTNTEVSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQ
SLLVNLRAMQNFLQLPEAERDRIYQDERERS-LNAASAMGPAPLISTPPSRPPQVKTATIATERNGKPEN
NTMNINASIYDEIQQEMKRAKVSQALFAKVAATKSQGWLCELLRWKEDPSPENRTLWENLSMIRRFLSLP
QPERDAIYEQESNAVHHHGDRPPHIIHVPAEQIQQQQQQQQQQQQQQQAPPPPQPQQQPQTGPRLPPRQP
TVASPAESDEENRQKTRPRTKISVEALGILQSFIQDVGLYPDEEAIQTLSAQLDLPKYTIIKFFQNQRYY
LKHHGKLKDNSGLEVDVAEYKEEELLKDLEESVQDKNTNTLFSVKLEEELSVEGNTDINTDLKD*

------------------------------

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End of modeller_usage Digest, Vol 5, Issue 63
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