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.
Message: 2 Date: Wed, 10 May 2006 12:52:11 -0700 From: Modeller Caretaker <> Subject: Re: [modeller_usage] specify sequence ranges for salign/align2d To: Douglas Kojetin <> Cc: Message-ID: <> 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.
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.
Message: 3 Date: Thu, 11 May 2006 10:23:06 -0400 (EDT) From: "Joydeep" <> Subject: [modeller_usage] ERROR: No alignment To: Message-ID:
<> 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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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--------------------------------------*