[Chimera-users] Querie: Ligand superimposition

Graziella Portelli graziellaportelli at gmail.com
Mon Sep 9 07:22:26 PDT 2013

Hi Dr Elaine

First of all thank you for your reply and I apologize for my delayed reply,
but was on a short break.
I 'll take a look at the discussion about superimposition; as that is what
I specifically need.

Once again, thank you for your kind explanation


On Fri, Sep 6, 2013 at 7:08 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Graziella,
> Not sure I understand the question, but you can display/undisplay any
> atoms that you want (without deleting) or you could delete the atoms you
> don't want. There are certainly many different ways you could do it, but
> the specifics would depend on the details of your data.  First I'll mention
> showing/hiding and then superposition.
> For example, you could hide the protein ribbons and atoms with commands:
> ~ribbon protein
> ~disp protein
> ... but there might still be other stuff you didn't want like water, so
> you would also have to hide those. These things could also be done with the
> menu instead of commands, but it would take more words to describe.
> Or, you could select only the atoms you want to show, and then use
> commands:
> sel invert
> ~ribbon sel
> ~disp sel
> You also mentioned you wanted to superimpose the ligands. Here is a
> discussion of the different ways to superimpose structures in Chimera, with
> links to the relevant manual pages ... the "match" command may be
> appropriate for your ligands:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> To learn about more general features like displaying/undisplaying atoms
> and ribbons, you may want to try the "getting started" tutorial
> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
> and take a look at command-line atom specification
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
> >
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Sep 6, 2013, at 5:26 AM, Graziella Portelli wrote:
> > Dear Chimera Team
> >
> > Hope this email finds you in good health.
> >
> > I am using UCSF Chimeria for my de Novo drug design disseration.
> > I am still learning the basic functions that this software offers,
> however have not been able to figure out the following.
> > Basically I need to put into one picture/frame the original ligand or my
> receptor and the possible ligands (generated by Ligbuilder). They have the
> same general structure with some changes and I need to superimpose them,
> but show them at separate levels. Is this possible to do this for only the
> ligands and not the receptor protein?
> >
> > I eagerly await your reply,
> >
> > Graziella Portelli
> > B.Pharm
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