I have a series of 3D structures built by MODELLER. I need top make
3D alignment of these structures because I need to see the
differences between these protein stuctures (they are from one family
of proteins) and the RMSD from RMS coordinates of the proteins. Which
scrip is better to use for it? There are 2 MODELLER scripts below.
Where in these scripts I need to put my PDB files. Fpr example I
have prot1.pdb, rpot2.pdb and prot3.pdb and 1-3.ali file. How such
script must look with these files?
I only see one script in your post, which looks like the standard SALIGN
multiple structure alignment example. The actual SALIGN calls probably
do not need to be changed - all you need to do is to provide an initial
alignment of the structures you're interested in. This is what is
currently done with the following part of the script:
This first creates an initial empty alignment, and then it runs through
the 'for' loop five times, each time reading in a single chain from the
given PDB file, and then adding the corresponding sequence to the
alignment (i.e. first the A chain from 1is4 is read, then the D chain
from 1uld, etc.) The sequences are simply added to the alignment - no
gaps are inserted.
In your case you could also create such a simple initial alignment with
something very similar, like:
aln = alignment(env)
for code in ('prot1', 'prot2', 'prot3'):
mdl = model(env, file=code+'.pdb')
aln.append_model(mdl, atom_files=code+'.pdb', align_codes=code)
Alternatively, if the 1-3.ali file you mention already contains an
initial alignment of the three proteins, you could just use that: