Re: [modeller_usage] build short 1000 olioopeptid from fasta file

[Modeller Caretaker <modeller-care@ucsf.edu>]

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@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage