[Chimera-users] using rmsd to compare ligand positions

[ARLEY REY PAEZ]

Ok, thanks very

Em qua., 29 de set. de 2021 às 12:47, Elaine Meng <meng at cgl.ucsf.edu>
escreveu:

> Hi Arley,
> The issue is how the atoms of the two copies are paired.  If the atoms to
> be matched with one another do not have the same atom names in #0 and #1,
> then simply saying "rmsd #0 #1" will give a higher value than expected.  To
> control the order in which they are paired, you may need to list the atoms
> individually in the command. Here is what it says in the help page for
> "rmsd":
> =-=
> If atom order is not specified, for example,
>
> rmsd #1:fad #0:fad
> rmsd #2:246,295 #0:195,221
>
> ...the atoms within a residue are ordered first by name, and where these
> are identical, by alternate location identifier, and where these are also
> identical, by serial number.
> =-=
> see: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
>
> To list the atoms individually in the command would look something like
> this, pretending my ligand residues are named XXX and YYY :
>
> rmsd #0:XXX at C1,C4,C3,C2,N  #1:YYY at C1,C2,C3,C4,N3
>
> ... would pair C1 of XXX with C1 of YYY, C4 with C2, C3 with C3, C2 with
> C4, and N with N3 to calculate the RMSD.
>
> Or, as also mentioned in the help page, you can select the atoms with the
> mouse (Shift-Ctrl-click) one by one in the same order first from #0 and
> then from #1 and then use command
>
> rmsd sel
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> > On Sep 29, 2021, at 7:35 AM, ARLEY REY PAEZ via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Best regard,
> > My name is Arley, I am a postgraduate student at the federal university
> of Lavras, Brazil.
> > I write this message because I have doubts about how to calculate the
> RMSD between two ligands after docking and redocking. My question is if
> Chimera works well to perform that calculation, since when for example I
> have two structures (ligands) that are, visually well superimposed and I
> calculate the value of RMSD with the use of the rmsd # 0 # 1 command, their
> value is high when compared With a structure that is not visually
> superimposed, why does that happen? Is it that chimera is not useful to
> carry out this task?
> > I appreciate you can help me with that concern.
> >
> > Att;
> >
> > Arley
>
>

-- 
Este e-mail foi enviado por um estudante da Universidade Federal de Lavras 
(UFLA). Caso esta mensagem possua algum conteúdo não apropriado, favor 
desconsiderá-la.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210929/c08257c8/attachment.html>