Superposition Help With Modeller
1
2
Entering edit mode
12.5 years ago
Harpalss ▴ 310

I am using the following code to generate a tetramer from a monomer using a tetramer template in Modeller.

Template tetramer = 2jgs.pdb Monomer = 2c4i.pdb

But my code only produces a monomer and not a tetramer.

env = environ()

#read pdb1 and pdb2 and creat and alignment between their sequences
aln = alignment(env)
mdl  = model(env, file='2jgs.pdb')
aln.append_model(mdl=mdl, align_codes='2jgs', atom_files='2jgs')
mdl2 = model(env, file='2c4i.pdb')

aln.append_model(mdl=mdl2, align_codes='model1', atom_files='model1')
aln.write(file='2jgs_2jgs.ali')


z = (mdl.chains)
for i in z:
    print i.name
    print len(i.residues)

# Genereate and save structure=structure alignment
    atmsel = selection(mdl.chains[i.name]).only_atom_types('CA')
    r = atmsel.superpose(mdl2, aln,)
    rms = r.rms
    drms = r.drms  

    mdl2.write(file='model1_fit22.pdb')
modeling • 2.2k views
ADD COMMENT
1
Entering edit mode
12.5 years ago
Harpalss ▴ 310

I found the solution to be very simple. The mdl2.write() method actually overwrites the previous structures, so all I had to do was change the variable name of the output and join the files together

ADD COMMENT
0
Entering edit mode

Dear,

Shall you add the modification of the code, since I did not understand what you change to let the code create tetramer.

Thank you
Mr. Maytham

ADD REPLY

Login before adding your answer.

Traffic: 2660 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6