Hi,
I have noticed that some HETATM records are read by Modeller and automatically handled as corresponding standard residues (for example MSE -> MET), even if env.io.hetatm is set to False. It is explained at http://salilab.org/modeller/9.9/manual/node171.html.
I would like to know if you could suggest a way to disable this behaviour and really ignore all HETATM records.
I have tried to remove the MSE line from restyp.lib and provide my reduced restyp.lib with env = environ(restyp_lib_file='myrestyp.lib'), but this does not seem to work as the MSE still appears to be read and taken into account as MET by Modeller.
Thanks for your time,
On 6/25/12 10:33 AM, Thomas Gaillard wrote: > I have noticed that some HETATM records are read by Modeller and > automatically handled as corresponding standard residues (for example > MSE -> MET)
Actually MSE -> MET is the only such translation done.
> I would like to know if you could suggest a way to disable this > behaviour and really ignore all HETATM records.
Unfortunately there isn't any way to do that - it is hardcoded into the PDB reader. Why do you want to treat MSE as HETATMs anyway? There may be a better way to achieve your goal.
Ben Webb, Modeller Caretaker
Le Monday 25 June 2012 à 03:41:56PM, Modeller Caretaker a écrit : > On 6/25/12 10:33 AM, Thomas Gaillard wrote: > >I have noticed that some HETATM records are read by Modeller and > >automatically handled as corresponding standard residues (for example > >MSE -> MET) > > Actually MSE -> MET is the only such translation done.
OK, I was saying "some HETATM records" because of the following paragraph in MODELLER manual, also mentioning MEX and ABU:
http://salilab.org/modeller/9.9/manual/node171.html
Some special handling is done for certain commonly-used modified residues. The MSE residue type is mapped to the regular MET amino acid, and the SE atom in this residue is mapped to SD. The MEX and ABU residue types are both mapped to CYS. In all cases, these residues are read as regular amino acids (ATOM records) regardless of whether they are marked as ATOM or HETATM in the PDB file. There is no need to turn on env.io.hetatm.
> >I would like to know if you could suggest a way to disable this > >behaviour and really ignore all HETATM records. > > Unfortunately there isn't any way to do that - it is hardcoded into > the PDB reader. Why do you want to treat MSE as HETATMs anyway? > There may be a better way to achieve your goal.
Because when MODELLER is integrated with other programs, some do not make the same choice of automatically treating HETATM MSE as ATOM MET and this can lead to confusion. I think this behaviour should not be hardcoded.
> Ben Webb, Modeller Caretaker
Additionnally, I think your mapping of MSE SE atom to MET SD atom is slightly incorrect in the eyes of the PDB standard:
HETATM XXXX SE MSE ... SE
should be mapped to:
ATOM XXXX SD MET ... S
and not to:
ATOM XXXX SD MET ... SE
The atom name format and element name are incorrect.
On 6/29/12 6:53 AM, Thomas Gaillard wrote: > OK, I was saying "some HETATM records" because of the following > paragraph in MODELLER manual, also mentioning MEX and ABU: > > http://salilab.org/modeller/9.9/manual/node171.html
Oh yes, I'd forgotten about the less common MEX and ABU cases. Yes, those are also mapped, to CYS.
> Because when MODELLER is integrated with other programs, some do not > make the same choice of automatically treating HETATM MSE as ATOM MET > and this can lead to confusion. I think this behaviour should not be > hardcoded.
Makes sense. I'll add an option to turn this off in the next release.
> Additionnally, I think your mapping of MSE SE atom to MET SD atom is slightly > incorrect in the eyes of the PDB standard:
Thanks for catching that - I will fix.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Thomas Gaillard