mais si il y a des assurances pour ça et s'il te plait, viens on essaye de bosser un peu sans y penser trop. Moi j'arrive pas à gérer. on verra bien ! Olivia Doppelt ----- Message d'origine ---- De : modeller_usage-request@salilab.org À : modeller_usage@salilab.org Envoyé le : Jeudi, 11 Mai 2006, 4h34mn 24s Objet : modeller_usage Digest, Vol 5, Issue 63 Send modeller_usage mailing list submissions to modeller_usage@salilab.org To subscribe or unsubscribe via the World Wide Web, visit http://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request@salilab.org You can reach the person managing the list at modeller_usage-owner@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: 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 _______________________________________________ Join Excite! - http://www.excite.com The most personalized portal on the Web!