[Chimera-users] Changing distance between two atoms

[Prathvi Singh]

Got it Elaine. Thanks 👍

On Fri, Mar 4, 2022, 9:39 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Prathvi,
> Moving is not guided by a specific distance, the whole model moves as a
> rigid body.  So all the distances would change, as you can probably see on
> the screen.  If you want to keep track of what some specific distances are,
> add measurements so that you can see them change while you move the model.
> Elaine
>
>
> > On Mar 3, 2022, at 10:46 PM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Just one last thing. When I move model-1 towards model-2 by 5Å, the
> distance between which two points of these two models gets manipulated?
> >
> > On Thu, Mar 3, 2022 at 11:13 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Prathvi,
> > I already described the only methods I know.  You would need to keep
> using the mouse or small "move" amounts until you achieve the distance you
> want.
> > Elaine
> >
> > > On Mar 3, 2022, at 3:57 AM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> > >
> > > Thank you Elaine for the reply. I was able to move one of my residues
> with respect to the other but the movement is not precise. The initial
> distance between the sidechain OG atoms of the SER residues was 8.925Å. I
> want the final distance to be 5.925Å. How to achieve this?
> > >
> > > On Wed, Mar 2, 2022 at 10:43 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > > Hi Prathvi,
> > > To move one set of atoms relative to another, you would need to
> > >
> > > (1) put them in two different models.  I.e. you could open all of this
> twice, and then delete Ser 10 from one copy and delete Ser 20 from the
> other copy.  Then you have one serine in each model.
> > >
> > > (2) Then measure the distance as you have already shown in your image.
> > >
> > > (3) Then move one model relative to the other.  You can do this by
> moving one model with the mouse after you "deactivate" (freeze) the other
> one.  Or, if you want to move exactly horizontal and avoid imprecise manual
> movements, then you could use the "move" command with the "models" option
> to specify only moving a specific model.
> > >
> > > Deactivating/activating and how it is done is explained here:
> > > <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
> > >
> > > "move" command:
> > > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>
> > >
> > > For example to move model #1 horizontally to the right 5 angstroms
> (without moving other models):
> > >
> > > move x 5 models #1
> > >
> > > You can move negative distances too.
> > > I hope this helps,
> > > Elaine
> > > -----
> > > Elaine C. Meng, Ph.D.
> > > UCSF Chimera(X) team
> > > Department of Pharmaceutical Chemistry
> > > University of California, San Francisco
> > >
> > >
> > > > On Mar 2, 2022, at 3:32 AM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> > > >
> > > > Hi Elaine,
> > > >
> > > > I have a PDB file which has two serine residues: SER10.A and
> SER20.A. The distance between their sidechain O-atoms (OG atoms) is 8.925Å.
> > > >
> > > > I want to bring the sidechain O-atom of SER10.A closer to the
> sidechain O-atom of SER20.A along an imaginary line which passes through
> the coordinates of these two atoms such that the distance between them gets
> reduced to 4Å. If I am thinking right, this would also require shifting the
> rest of the atoms of SER10.A towards SER 20.A in a similar manner. Is it
> possible to achieve this in chimera? I am attaching a screenshot just for
> reference.
> > > >
> > > > Thanks anyways and regards
> > > > --
> > > > Prathvi Singh,
> > > > Research Fellow,
> > > > Department of Biological Sciences & Bioengineering,
> > > > Indian Institute of Technology, Kanpur-208016
> > >
> > >
> > >
> > > --
> > > Prathvi Singh,
> > > Research Fellow,
> > > Department of Biological Sciences & Bioengineering,
> > > Indian Institute of Technology, Kanpur-208016
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> >
> >
> >
> > --
> > Prathvi Singh,
> > Research Fellow,
> > Department of Biological Sciences & Bioengineering,
> > Indian Institute of Technology, Kanpur-208016
> > _______________________________________________
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> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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>
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