[modeller_usage] Re : modeller_usage Digest, Vol 5, Issue 63

-- 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!