Thanks for suggestion!
I've already done this placing '.' instead of '_' at the end of the sequence but the result was the same error which might indicate that ligand could not be found in template PDB where it present at the end of the sequence as the HETATM.

Also I wounder to know

1) How I could easily convert alignment in FASTA done by the external servers to the modeler PIR format ?
2) how I could precisely define salt bridges between selected residues in the residues (or simply take it from the template with the homology cysteins in the same positions)?

Thanks for help,

James


2014-04-15 15:13 GMT+04:00 Lalith Kumar <lalithkumar07@gmail.com>:
The heteroatom tag . is missing in the Query of your interest. Please place it at the end of your alignment (i.e., after HSP like this HSP.) in query.


On Tue, Apr 15, 2014 at 2:35 PM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Modeller users!

I've followed 1st modeller tutorial making alignment of my target against 1 template (with the inclusion of hetatm from the template). As the result I've obtained the below alignment


>P1;2rh1A
structureX:2rh1.pdb:  29 :A:+283 :A:::-1.00:-1.00
---------DEVWVVGMGIVMS----------LIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGL
AVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWI
VSGLTSFLPIQ-MH--WYRATHQE-----AINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEA
KRQLKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYC-RSPDF
RIAFQELLCL------.*

>P1;od_r
sequence:od_r:     : :     : ::: 0.00: 0.00
MEGKNLTSISECFLLGFSEQLEEQKPLFGSFLFMYLVTVAGNLLIILVIITDTQLHTPMYFFLANLSLADACFVS
TTVPKMLANIQIQSQAISYSGCLLQLYFFMLFVMLEAFLLAVMAYDCYVAICHPLHYILIMSPGLCIFLVSASWI
MNALHSLLHTLLMNSLSFCANHEIPHFFCDINPLLSLSCTDPFTNELVIFITGGLTGLICVLCLIISYTNVFSTI
LKIPSA-QGKRKAFSTCSSHLSVVSLFFGTSFCVDFSSPSTHSAQKDTVASVMYTV--VTPMLNPFIYSLRNQEI
KSSLRKLIWVRKIHSP-*

where Od_r is the modeled protein and 2rh1 is the template consisted of ligand ('.' in aliugn file)

now I'm running script for making models (where ligand should be included from the template and obtain error about atom mismatches

from modeller import *
from modeller.automodel import *


# Read in HETATM records from template PDBs
env.io.hetatm = True
env.io.hydrogen= True
# directories for input atom files
env.io.atom_files_directory = ['.', './results']

env = environ()
a = automodel(env, alnfile='result.ali',
              knowns='2rh1A', sequence='od_r',
              assess_methods=(assess.DOPE,
                              assess.GA341))
a.starting_model = 1
a.ending_model = 10
a.make()

    return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and  pdb files are different:      283      282 For alignment entry:        1  2rh1A

how it could be fixed and obtain models with the ligands in the positions identical to the templates ?


James

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--
Lalith Kumar K
Research Associate,
CADD Division,
Dr. Reddy's Institute of Life Sciences (Formerly known as Institute of Life Sciences)
University of Hyderabad Campus
Gachibowli, Hyderabad 500046, India
Tel: +91 9502074040