[Chimera-users] building and positioning disordered sequence

thereal sisterdot therealsisterdot at gmail.com
Wed May 4 01:08:05 PDT 2016


Thanks a lot Elaine!

If i should find a solution i will make sure to post it!

all the best!

On Tue, May 3, 2016 at 8:40 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear sisterdot,
> Hmmm, this would probably be extremely difficult in Chimera.  There isn’t
> really a way to place residues and then say “build linkers to connect these
> residues in their current positions.”  Although we do have an interface to
> “missing segment” peptide building with Modeller, that is typically for
> missing loops when you already have coordinates for most of a structure.
> The problem is that to use that feature, you would need:
>
> (1) the sequence of the whole thing including the lysines open in
> Multalign Viewer
> (2) the existing coordinates correctly associated with that sequence,
> which is practically automatic when you already have most of the protein,
> but I don’t think it is even possible for individual free-floating residues
>
> … and even if you had both of those, if I remember correctly, the building
> would not automatically avoid the other chain (the PDB structure) and might
> severely overlap with it.  Here’s the docs about building missing loops.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building
> >
>
> Yet another approach would just be to build a long strand or a long helix
> in the sequence of your unstructured protein, and then manually drag all or
> parts of it, and manually rotate backbone torsional angles, to try to get
> the lysines in the correct vicinities.  However, this would probably drive
> you crazy in rather short order.  For building the peptide de novo, see
> Build Structure (Start Structure section), for moving the whole thing or
> parts of it, see Movement Mouse Moude, and for rotating torsions, see
> Adjust Torsions.  Then you could try to fix up any severe distortions with
> Minimize Structure.
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start
> >
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust
> >
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.html
> >
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html
> >
>
> Sorry to be discouraging, just didn’t want to send you on a wild goose
> chase!  But maybe others have some simpler ideas, or can suggest some other
> program(s) better suited to the task…
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> > On May 3, 2016, at 1:31 AM, thereal sisterdot <
> therealsisterdot at gmail.com> wrote:
> >
> > Dear Chimera Users,
> >
> > i would like to do something in chimera, that is not exactly science but
> more graphics :-)
> >
> > i have a known structure with 5 positions that i know are crosslinking
> to a 100aa intrinsically disordered partner sequence.
> >
> > now just in order to better imagine how the disordered binding partner
> wraps around the structure, i would like to put 5 lysines in the open space
> near the known crosslinking positions in the pdb structure, and than
> somehow build the rest of the disordered partner sequence connecting those
> lysines.
> >
> > its not about getting a estimate of the structural arrangement of the
> partner.
> > its just so i can better imagine how the partner sequence extends around
> the interacting residues (as the residues are not in a patch but really all
> over the 100 aa) or if the arrangement would be sterically possible.
> >
> > any ideas if and how i could achieve that in chimera ? i know that is
> sound more like a task for illustrator, but :-)
> >
> > THANKS A LOT!!!
> > sisterdot
>
>
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