[Chimera-users] Question about peptide connection

Tue Jul 27 08:30:58 PDT 2021

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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