Re: [modeller_usage] HETATM reading

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 2/6/11 2:04 PM, Seth Tanner wrote:
> I have a HETATM entry at the end of one of my protein chains.
> I have included the "env.io.hetatm = True" statement in my code. I have
> also included "." residues in my alignment file for each HETATM residue
> and formed a separate chain out of them using the "/" separator. I did
> this in both the template sequence and in the sequence to be modelled.
> However, I still get the following error:
> --
> read_te_290E> Number of residues in the alignment and  pdb files are
> different:     1566     1560
>                For alignment entry:        1 1GWP.pdb
>                                   x  (mismatch at alignment position   1561)
>   Alignment   KLFHIRTGNMDTYYWHRYT..
>           PDB   KLFHIRTGNMDTYYWHRYT
>         Match   ********************
> --
> It appears that Modeller cannot read the HETATM entries in the PDB file.
> I wonder if anyone has a suggestion.

Without seeing your actual input files it is impossible to be sure what 
your problem is, but perhaps you have a range set up in your alignment 
header: see
https://salilab.org/modeller/9v8/manual/node454.html

For example, the header
structureX:5fd1:1    :A:106  :A::: 1.90: 0.19
instructs Modeller to read residues 1:A through 106:A from the PDB file. 
So if "106:A" is before your HETATM, Modeller won't read it. Simply 
update the end of the range to match the residue number (or remove the 
range entirely to have Modeller read the whole file).


	Ben Webb, Modeller Caretaker
--
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