Thank for the script. I have collected into a module to get a smaller file. All my seqeunces files is build except the one I am sending. I get this error message. The seqeunces is sent as attachment and as the following patter MLXP where the third aminoacid can be anything.

Best regards
Knut J


              Number of sequences in the alignment:        1
Traceback (most recent call last):
  File "/home/knut/workspace/ligand_petide/src/create_seqeunce.py", line 35, in <module>
    buildseqeunce('hNatE.txt','hNatE')
  File "/home/knut/workspace/ligand_petide/src/create_seqeunce.py", line 27, in buildseqeunce
    mdl.build_sequence(line.rstrip('\n'))
  File "/usr/lib/python2.6/dist-packages/modeller/model.py", line 133, in build_sequence
    self.generate_topology(a[0], patch_default=patch_default)
  File "/usr/lib/python2.6/dist-packages/modeller/model.py", line 238, in generate_topology
    self.env.libs.modpt, alnseq._num, patch_default)
_modeller.ModellerError: generat_477E> No templates in the alignment. Number of sequences in the alignment:        1




from modeller import *


def buildseqeunce(filename,out):
    env = environ()
    aln = alignment(env)
    mdl=model(env)

    env.libs.topology.read('${LIB}/top_heav.lib')
    env.libs.parameters.read('${LIB}/par.lib')
   
    file=open(filename,'r')
   
  
   

   
    for (n, line) in enumerate(file):
       
       
        mdl.build_sequence(line.rstrip('\n'))
        mdl.write(file=out + "%g.pdb" %n)
    file.close()   
 

buildseqeunce('hNatE.txt','hNatE')
















> Date: Tue, 6 Apr 2010 15:39:34 -0700
> From: modeller-care@salilab.org
> To: knutjbj@hotmail.com
> CC: modeller_usage@salilab.org
> Subject: Re: [modeller_usage] build short 1000 olioopeptid from fasta file
>
> On 04/06/2010 06:24 AM, Knut J Bjuland wrote:
> > I have 1000 or more short peptid seqeunce which are 4 amino acid long.
> > Can I use modeller to build them just as a linear structure without any
> > 3d structure.
>
> If by "linear structure without any 3d structure" you mean an extended
> chain, then sure, you can use model.build_sequence():
> http://salilab.org/modeller/9v7/manual/node166.html
>
> As an example, if your 1000 sequences are in a file called seqs.txt, one
> per line, then the following script will make a set of PDB files, one
> for each sequence:
>
>
> import modeller
>
> env = modeller.environ()
> env.libs.topology.read('${LIB}/top_heav.lib')
> env.libs.parameters.read('${LIB}/par.lib')
>
> for (n, line) in enumerate(open('seqs.txt')):
> mdl = modeller.model(env)
> mdl.build_sequence(line.rstrip('\r\n'))
> mdl.write(file='seq-%d.pdb' % n)
>
>
>
>
> Ben Webb, Modeller Caretaker
> --
> modeller-care@salilab.org http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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