W> MODEL atom not classified: GLY:OXT GLY
Dear Modellers,
I am trying to build some missing loops in a PDB structure with modeller 9v4. For this, I am using the script found in examples/automodel/model-loop-define.py for which I only changed residue_range's, and alnfile, knowns and sequence. The protein is a dimer, and both subunits end with a Gly residue.
I am getting this warning at the DOPE potential assessment: >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: GLY:OXT GLY iatmcls_286W> MODEL atom not classified: GLY:OXT GLY
A related message in the archives suggests editing modlib/atmcls-melo.lib (http://www.salilab.org/archives/ modeller_usage/2004/msg00169.html). This file seems to be used for loop modelling, but not for DOPE evaluation, as suggested in the log file: openf___224_> Open ${LIB}/atmcls-mf
I have also tried to use the dope_loopmodel class, instead of loopmodel. Here, I get the same warnings for both stages (loop modelling and DOPE assessment).
How can I avoid such messages? Should I somehow edit atmcls-mf.lib?
Many thanks, Rui Rodrigues
-- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)
Joaquim Rui Rodrigues wrote: > I am getting this warning at the DOPE potential assessment: >>> Model assessment by DOPE potential > iatmcls_286W> MODEL atom not classified: GLY:OXT GLY > iatmcls_286W> MODEL atom not classified: GLY:OXT GLY
That's fine - it just means that the DOPE potential has no parameters for terminal oxygens. That's because no such atoms were included in the training set for the potential. So these warnings are normal and are nothing to worry about.
> A related message in the archives suggests editing modlib/atmcls-melo.lib (http://www.salilab.org/archives/ > modeller_usage/2004/msg00169.html).
No, that's for the older loop modeling potential, which *does* have parameters for terminal oxygens. That mailing list post merely addressed the change in PDB atom naming for terminal oxygen from OT1/OT2 to OXT.
> This file seems to be used for loop modelling, but not for DOPE > evaluation
Exactly - the older loop modeling potential is used only for loop modeling. DOPE is used both for loop modeling and for model assessment.
> How can I avoid such messages? Should I somehow edit atmcls-mf.lib?
The warnings are normal, so there is nothing you need to do.
Ben Webb, Modeller Caretaker
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Joaquim Rui Rodrigues -
Modeller Caretaker