[modeller_usage] Including hetatm when hetatm does not immediately follow ATOM list

[Shuo Huai Johnny Wu <>]

Hi

I am trying to thread a target rhodopsin sequence from humans to the
template bovine rhodopsin structure (pdb1f88).

The rhodopsin crystal structure exists in the pdb file as a crystal
dimer represented by chain A and B. Each chain is 348 amino acids, but
there are missing residues on both chains.

 I used the simple automodel script, and it worked well. When I tried
to include both the ligands and the carbohydrates (hetatms) into the
structure by setting env.io.hetatm = True, I get errors that do not
make much sense to me. My structure pdb is different from the hetatm
example pdb for in that the ligands hetatm residue numbers do not
immediately follow the atom residue sequence.

Here is a summary of the heteroatoms that follow the seqres

HET    NAG  A 501      14
HET    NAG  A 502      14
HET    NAG  B 601      14
HET    NAG  B 602      14
HET    MAN  B 603      11
HET    NAG  A 701      14
HET    NAG  A 702      14
HET    NAG  B 801      14
HET    NAG  B 802      14
HET     HG  A 901       1
HET     HG  B 902       1
HET     HG  A 903       1
HET     HG  B 904       1
HET     HG  A 905       1
HET     HG  B 906       1
HET     ZN  A 907       1
HET     ZN  B 908       1
HET     ZN  B 909       1
HET     ZN  A 910       1
HET    RET  A 977      20
HET    RET  B 978      20

There are no amino acids residue numbers that flank the hetam numbers.
That is, there is no amino acid numbers from 803 to 900. These entries
are left unspecified.

All hetatms are described after chain B in the ATOM section.

ATOM   5067  OD1 ASN B 326      30.599  31.795  -7.049  1.00107.30           O
ATOM   5068  ND2 ASN B 326      30.914  33.473  -8.519  1.00107.62           N
TER    5069      ASN B 326
HETATM 5070  C1  NAG A 501      37.620   3.757 -28.808  1.00 65.21           C
HETATM 5071  C2  NAG A 501      38.420   5.021 -29.058  1.00 65.24           C
HETATM 5072  C3  NAG A 501      37.477   6.163 -29.455  1.00 66.66           C

I first tried to include all hetatms as '.' with the unspecified
residues past the end of the protein (aa 348) replaced with '-'.

>P1;B._taurus
structureY:B._taurus:1    :A:  977:A:ground state rhodopsin:Bovine: :
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLA
VADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFT
WVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA----S
ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTT
LCCGKNP------STTVSKTETSQVAPA----------------------------------------------------
--------------------------------------------------------------------------------
--------------------..----------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------..------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------.-.-.----.--------------------------------------------------
----------------.*

It results in this error:

_modeller.ModellerError: read_te_290E> Number of residues in the
alignment and  pdb files are different:      347      650 For
alignment entry:        1  B._taurus

When I forgo the trailing '-' and simply append hetatms to the end in
a series of '.':

>P1;B._taurus
structureY:B._taurus:1    :A:  977:A:ground state rhodopsin:Bovine: :
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA----SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNP------STTVSKTETSQVAPA........*

I get the following error:

_modeller.ModellerError: read_te_290E> Number of residues in the
alignment and  pdb files are different:      347      650 For
alignment entry:        1  B._taurus


I've seen the following thread and tried to follow the advice
enclosed, but I am still having trouble.
http://salilab.org/archives/modeller_usage/2008/msg00183.html
http://salilab.org/archives/modeller_usage/2008/msg00186.html

The structure ID of bovine rhodopsin is pdb1f88.

Thanks in advance,
-- 
Shuo Huai Johnny Wu



-- 
Shuo Huai Johnny Wu