Hi,
I have download a crystal structure having 8 missing residues in it. I build these missing residues using modeler missing residue script but it ignored my all water atom. i add one line in that script i.e. env.io.water as well as dot character in the alignment file but when i ran it give me the following error.
please guide me, how i can solve my problem.
File "model_single.py", line 20, in ?
a.make()
File "/usr/physics/biophys/MODELLER/modeller-9.14/modlib/modeller/automodel/loopmodel.py", line 37, in make
automodel.make(self, exit_stage)
File "/usr/physics/biophys/MODELLER/modeller-9.14/modlib/modeller/automodel/automodel.py", line 110, in make
self.homcsr(exit_stage)
File "/usr/physics/biophys/MODELLER/modeller-9.14/modlib/modeller/automodel/automodel.py", line 488, in homcsr
self.check_alignment(aln)
File "/usr/physics/biophys/MODELLER/modeller-9.14/modlib/modeller/automodel/automodel.py", line 470, in check_alignment
aln.check()
File "/usr/physics/biophys/MODELLER/modeller-9.14/modlib/modeller/alignment.py", line 208, in check
self.check_structure_structure(io=io)
File "/usr/physics/biophys/MODELLER/modeller-9.14/modlib/modeller/alignment.py", line 217, in check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb
Just align the result pdb to original pdbs, and save the result pdb & original water to a pdb.
Pymol 1.7 can do it.
I agree with Chen. The easiest is just to use pymol. 1.align the pdbs in pymol. 2. Select homology model. 3. Select water molecules from original pdb. 4. save selection. done!
I also agree with Chen.
By the way, the residues might have been missed as the region is disordered
and the modeled structure might not be that reliable.
So you must be cautious if the structure is important in your analysis.
Note that the water structure of many PDB entries is quite terrible. If you really need it, you'd better check it in the context of the electron density. This is easy in COOT. You can download the PDB model and electron density maps from EDS (just give it the PDBid) or an updated model + maps from PDB_REDO directly.
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