drugdesign wrote: > 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:
> aln = alignment(env) > for (code, chain) in (('1is4', 'A'), ('1uld', 'D'), ('1ulf', 'B'), > ('1ulg', 'B'), ('1is5', 'A')): > mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) > aln.append_model(mdl, atom_files=code, align_codes=code+chain)
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:
aln = alignment(env, file='1-3.ali')
Ben Webb, Modeller Caretaker