[Chimera-users] how to display specific residues and atoms in chimera

[Elaine Meng]

Hi Abir,
There are so many possible ways I have trouble deciding how to answer!

The shortest way to answer is to give some commands, so I'll start with that.  Choose "Command Line" from Favorites menu to show the command line.  The following are example commands and explanations:

~display
(hide all atoms, bonds, and nucleotide objects; ribbon will still be there)

~ribbon
(hide all ribbon, if you wanted to do that)

ribbon
(show all ribbon)

~ribbon :2-28.a
(hide only the ribbon for residues 2-28 of chain A)

disp :56.a,78.a,10-15.a,47.b,53.b
(display residues 56, 78, and 10-15 in chain A, and 47 and 53 in chain B)

disp :37.b,33.b at c1',c2',c3',c4',o4',o2',o3',c5',o5'
(display specific ribose atoms of residues 33 and 37 in chain B)

Here is the documentation on how to specify atoms and residues in commands:
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

With the menu and graphical interfaces, you could do the same stuff (except it is easier to give specific atom names in the command line).  The general approach with the menu and graphical interfaces is to first make a selection and then use the actions menu on the selection.  For example, you could show Sequence (favorites menu), then drag with the mouse in the sequence to select residues to display, then use menu: Actions... Atoms/Bonds... display

You can select things with the select command too, for example
select :56.a,78.a,10-15.a,47.b,53.b

Finally you may wish to to show atoms instead of the nucleotide objects, or change the style of the nucleotide objects.  To show "regular" atoms instead of nucleotide objects, command:

nuc side atoms
(or menu: Actions... Atoms/Bonds... nucleotide objects... off)

To change the style of the  nucleotide objects, choose menu: Actions... Atoms/Bonds... nucleotide objects... settings, and try different settings in that panel.  By default "Apply" on that nucleotides panel will only affect the selected residues, or if nothing is selected, will affect all residues.  Nucleotide styles include "ladder" and lollipops (show sugar/base as tube/slab and slab object "ellipsoid" instead of box).  "Show base orientation" controls whether the slab has bumps on it.  For details on this tool and available styles click the Help button on the dialog, or look here:
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/nucleotides/nucleotides.html>

You might want to take a look at some of the tutorials.
Getting started:
<http://plato.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
User's Guide tutorials index (actually you can get to all these from the Chimera Help menu):
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
This image tutorial includes showing only the important residues; it is about proteins but the approach is basically the same for nucleic acids.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html>

I hope this helps,
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 Oct 7, 2011, at 8:33 PM, Abir wrote:

> Hello, 
> I am new to chimera. I am trying to make an animation of an actual reaction. I have the frames saved as pdbs. I guess one can use the MD movie tool to make the animation in chimera. However, I want to show only specific residues and atoms from my active site in the movie and not the entire system (my system is a ribozyme).  I played with chimera for a while, but could not figure out how to do that. 
> It will be great if I get some help regarding this issue. 
> Thanks a lot. 
> Regards, 
> Abir