[Chimera-users] Querie: Ligand superimposition
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
> 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:
> To learn about more general features like displaying/undisplaying atoms
> and ribbons, you may want to try the "getting started" tutorial
> and take a look at command-line atom specification
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users