[Chimera-users] Question about peptide connection

Tue Jul 27 10:08:47 PDT 2021

Hi Elaine,

That makes a lot of sense, thank you very much for your help.

On Tue, Jul 27, 2021 at 11:31 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Nicole,
> Personally I wouldn't recommend using the total energy values.  They are
> calculated to get a gradient to allow minimization, but the specific total
> quantities aren't that meaningful.  Tiny movements can make a huge
> difference in the value and you don't know the "shape" of the whole
> multidimensional energy landscape.
>
> Modeller includes optimization (e.g. see <
> https://salilab.org/archives/modeller_usage/2009/msg00162.html>) so you
> don't need to minimize afterwards, and also various model scores that
> Modeller  and/or the Sali lab Model Evaluation Server gives are probably a
> more relevant measure of the quality of the result than some energy value.
>
> Model scores that may be reported:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html#modellist>
>
> Also Modeller puts a confidence value per residue in the bfactor column,
> so if you color the resulting model by "bfactor" you can see which areas
> are more or less well modeled.  e.g. command
>
> rangecolor bfactor,r min blue mid white max red
>
> would show less reliable parts as red.  The value is described here:
> <https://salilab.org/archives/modeller_usage/2003/msg00164.html>
>
> However, it may not add more information to what you already know, that
> the part that you changed is not in the template, so it will be scored as
> less reliable because less information was used to generate it.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jul 27, 2021, at 7:25 AM, Nicole Ostrovsky via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > The modeller tool seems to be working for me, thank you very much! I
> will email again if any problems arise with it.
> >
> > One more question - is there a command or a tool I can use to find the
> internal energy of a peptide? I have been running a 1 DS 0 CGS minimization
> which means my peptide moves just slightly but I'm wondering if there is a
> better way to do it.
> >
> > Nicole Ostrovsky
> >
> > On Mon, Jul 26, 2021 at 6:24 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Thanks, Marco -- good idea!  It might give a more reasonable result than
> manual building + minimization.
> >
> > Nicole, see:
> > <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative
> >
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
> >
> > Elaine
> >
> > > On Jul 26, 2021, at 2:58 PM, Marco Sette via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> > >
> > > Hi Nicole,
> > >
> > > you could  note the pdb name of the old structure and use the homology
> modelling tool provided in Chimera (it is based on Modeller then you need a
> password to access the server) to model the new sequence, using the old one
> as a template. Check that the alignment is correct (identical alignment
> except the new region) and let the server prepare your structure.
> > >
> > > Hope it helps,
> > >
> > > Regards,
> > >
> > > Marco
> > >
> > >
> > >
> > > Il 26/07/2021 21:19, Nicole Ostrovsky via Chimera-users ha scritto:
> > >> Hello,
> > >>
> > >> I have a structure which I've cut a section out of and I am working
> on connecting the two loose ends together. I wanted to connect them with
> two glycine residues - since they are easiest to work with and have no side
> chains. I am doing this using the Modify Structure option under the Build
> structure tool and adding one atom at a time. However, when I try to
> minimize my newly created glycine, I get the error message "No MMTK name
> for atom "H1" in standard residue "GLY"" (I've attached a picture of my
> reply log). I'm not sure how to troubleshoot this.
> > >>
> > >> Is there a better way to connect two ends of a peptide, or should I
> change the way I am using the modify structure tool?
> > >>
> > >> Thank you.
> > >>
> > >> Nicole Ostrovsky
> > >>
> > >>
> > >> _______________________________________________
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> > > --
> > > Dr.Marco Sette, Ph.D.
> > > Department of Chemical Sciences and Technology
> > > University of Rome, "Tor Vergata"
> > > via della Ricerca Scientifica, 00133, Rome, Italy
> > > e-mail:
> > > sette at uniroma2.it
> > >
> > > e-mail:
> > > m77it at yahoo.it
> > >
> > > Tel.: +39-0672594424
> > > Fax: +39-0672594328
> > >
> > > http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
> > >
> > >
> > >
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