On Tuesday, 14 June 2016 12:55:30 AM chemocev marker wrote:
> Thanks for your suggestions,
> Well in case of 2 cis-peptide, there is no electron density and B-factor is
> very high. They are in favorable region of Ramachandran plot. I have to
> look at them very carefully.
Have you looked to see if there are homologous structures that also
have cis-peptides at those positions?
Ethan
> I would like to model them differently and would like to see how they
> behave in energy minimization with short MD simulations.
> best
> Jiri
>
> On Tue, Jun 14, 2016 at 12:14 AM, Tristan Croll <[log in to unmask]>
> wrote:
>
> > Hi Jiri,
> >
> > I agree with Paul that you need to make sure these are actually wrong
> > before "fixing" them. Definitely look at them in the context of the map for
> > a start, and study their local environment remembering that cis-peptide
> > bonds need to be quite strongly stabilised to become favourable. As a rough
> > rule of thumb you'd expect both the hydrogen and oxygen in the peptide bond
> > to be involved in good H-bonds, and/or lots of steric crowding acting to
> > prevent the trans conformation. If neither criterion is met, I'd say it's
> > most likely wrong.
> >
> > VMD does have a plugin (accessible from the Modelling menu) that can check
> > for and semi-automatically correct cis bonds. For each bond it will ask to
> > to select either the hydrogen or the oxygen to move to the other side of
> > the backbone, then run a brief NAMD energy minimisation of the local area
> > to regularise the geometry.
> >
> > If the cis bonds do turn out to be incorrect, though, I'd suggest you may
> > have other things to worry about. What do the other stats (Ramachandran
> > outliers, clashscore, sidechain outliers) look like? What sort of
> > resolution are we talking about? If you have incorrect cis bonds, chances
> > are there are other less-easily spotted problems that may mess with any
> > simulation.
> >
> > Best regards,
> >
> > Tristan
> >
> >
> >
> > Tristan Croll
> > Lecturer
> > Faculty of Health
> > School of Biomedical Sciences
> > Institute of Health and Biomedical Engineering
> > Queensland University of Technology
> > 60 Musk Ave
> > Kelvin Grove QLD 4059 Australia
> > +61 7 3138 6443
> >
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> >
> > > On 14 Jun 2016, at 3:29 AM, chemocev marker <[log in to unmask]>
> > wrote:
> > >
> > > HI All
> > > I have some residues in my x-ray structure with the high B-value and
> > they make cis peptide. Is there is option either in Pymol or in VMD viewer
> > to correct them automatically if I want to use the X-ray structure for
> > input in simulations experiment.
> > >
> > > best
> > > Jiri
> >
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