[Chimera-users] Changing distance between two atoms

[Prathvi Singh]

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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