[Chimera-users] Molecular Dynamics Simulation RMSD for only spesific atoms

[Barış KURT]

Thank you so much. it worked. (I used this command for 2-1-60-61 dihedrals
: sel @/serialNumber=2 | @/serialNumber=1 |
@/serialNumber=60|@/serialNumber=61)
Thank you again.
Baris


Eric Pettersen <pett at cgl.ucsf.edu>, 7 Eyl 2022 Çar, 19:44 tarihinde şunu
yazdı:

> Hi Barış,
>         The RMSD plot only plots all atoms if none are selected.  Is the
> problem that you don't know how to select the desired atoms -- maybe
> because they have duplicate names?  There are several alternatives.  If we
> are talking about a very small number of atoms, you could just select them
> with the mouse -- control-click the first, then shift-control-click the
> second, third, fourth, etc.  Obviously, for any large amount of atoms this
> would be tedious.  You can also use commands to select by element type or
> atom serial number.  Here are example commands:
>
> Select elements Pd, Cl, and C:
>
>         sel @/element=Pd | @/element=Cl | @/element=C
>
> Select atom serial numbers 7 through 10:
>
>         sel @/serialNumber>=7 & @/serialNumber<=10
>
>
> The '|' in the first command forms the union between its left and right
> sides.  Conversely, the '&' in the second command takes the intersection of
> its left and right sides.
>
> --Eric
>
>         Eric Pettersen
>         UCSF Computer Graphics Lab
>
>
> > On Sep 7, 2022, at 6:26 AM, Barış KURT via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> > my intention is to plot RMSD chart for only Pd,Cl,Cl,C atoms (their
> numbers are 1,2,3,4). But I couldn't find a way to do it.Also II want to
> plot dihedral RMSD for all atoms except C,H,Cl,P atoms.How can I do that?
> > Thank you
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