[chimerax-users] Aligning small molecules, ligands

[Noriega, Heather]

Hello,

Yes, I did try to go off a couple of the examples. (i.e.  atoms named N,
CA, C, O in chain A) with the align command but I was missing certain
classifiers I believe it said. The commands you used did help, as it gave a
reference to go off of to start rotating bonds to create what I needed.
Also, I used a text editor to fix the residue names. Thank you Elaine, I
appreciate it.


Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
Howard University
heather.noriega at bison.howard.edu
520-203-1883


On Fri, Mar 11, 2022 at 12:05 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Heather,
> You would specify the atoms directly in the command line.  How to specify
> atoms in commands is explained here:d
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
>
> Actually if you would click the "matchatoms" or "refatoms" link in the
> help page for "align," it would show you that page anyway, which has
> several examples.   Did you try anything yourself?
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
>
> Issues I see are that
>
> (1) your model #1 has two copies of the PEG.  Which one are you trying to
> align with #2?   By holding the  mouse over some atom in each copy I can
> see that one is chain C (reported as #1/C in pop-up info balloon) and the
> other one is chain D.  All three of them have the same residue name, UNL.
>
> (2) your model #2 has hydrogens but #1 does not.  You need to have equal
> numbers of "matchatoms" and "refatoms" so you would either need to delete
> the hydrogens or a use a specification that excludes them
>
> Starting from your session I used these commands
>
> delete H
> align #2 to #1/C
> [.... or to do it for the other copy ...]
> align #2 to #1/D
>
> None of this cares what is selected, i.e. those commands don't use the
> concept of selection.
> 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 11, 2022, at 8:04 AM, Noriega, Heather via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> > I hope you are well Elaine. I am wondering if there is a way to align my
> combined model UNL to my model 2. In hopes this could be a reference model
> of my docking done in Chimera for future builds. I did figure out the
> bonding, thank you. :)
> >
> > I attached the session, and have read the align command. I am just
> unsure how to manipulate it to superimpose the ligand.
> >
> > align matchatoms (the whole model 2) toAtoms (UNL on model 1).
> > Thanks for your help.
>
>
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