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

[Eric Pettersen]

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
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users