[Chimera-users] viewing & comparison of multiple overlay structures

Eric Pettersen pett at cgl.ucsf.edu
Tue Apr 3 16:57:06 PDT 2007

On Apr 3, 2007, at 1:47 PM, Roberta King wrote:
> First, After overlaying multiple protein (pdb) structures with  
> ligands using MultiAlign based on alignment, how does one easily  
> view only the overlaid ligands? [Note: I have up to 36 structures  
> overlaid, each with 0-2 ligands.]
Hi Roberta,
	Using the command line (Favorites->Command Line), typing "~disp;  
show ligand" will hide all structures and then show only the  
ligands.  If every structure had a ligand you would only need "show  
ligand" since the show command hides parts of structures that aren't  
to be shown, but if no part of a structure matches the show criteria,  
the structure isn't changed -- so you need the "~disp" also to  
guarantee that ligand-less structures get hidden.
	This is also doable with the menus by Select->Structure->ligand  
followed by Select->Invert Selection (or shift-right-arrow instead to  
invert the selection in all models) and then Actions->Atoms/Bonds->hide.
	From there, you will probably want to select the ligand clump by  
control dragging the mouse across the clump (there will be a green  
box outline as you drag the mouse) and then use Actions->Focus to  
zoom in on the clump and make it the center of rotation.
>  Secondly, can chimera then calculate a solvent-accessible closed  
> surface for the protein cavity surrounding each ligand?  
> Alternatively, I could calculate the cavity first, then overlay  
> based on alignment. The goal is to view the overlaid cavities for  
> visual comparison.
	It depends.  If the cavity is actually completely enclosed then  
Chimera won't depict it.  If there is some channel to the binding  
pocket, then it should be depicted.  I say "should" because the  
surfacing library we are currently using (MSMS) is known to have  
problems when there are narrow channels in a surface.  We are working  
on a replacement library that should solve both these problems, but  
it's not ready yet.  Providing that MSMS doesn't fail, your pockets  
should be depicted. It is also sometimes possible to work around the  
MSMS problem by adding hydrogens to a structure or by slightly  
changing VDW radii (with the vdwdefine command) -- but you have to do  
this before any surfaces fail because after a failure surfacing won't  
work again until you restart Chimera.
	You create a surface with Actions->Surface->show or the "surf"  
command.  If with experience you know that surfacing certain models  
is problematic, you can restrict the surfacing to particular models  
by selecting them before using the menus or providing the model  
numbers as arguments to the surf command (e.g. "surf #0,3-7,9").
>  Thirdly, can chimera calculate electrostatic charge on amino acids  
> surrounding a binding cavity and reflect that charge onto the  
> closed cavity surface? Can this surface be included in overlay view?
	You can use the Add Charge tool (in the Structure Editing category)  
to add partial charges to all atoms.  You can then use the Render By  
Attribute tool (Structure Analysis category) to color the surface and/ 
or atoms based on the partial charges.
	For more precise electrostatics, you can use an external tool such  
as APBS or Delphi to generate an electrostatic grid, and open that in  
Chimera and then use the Electrostatic Surface Coloring tool (Surface/ 
Binding Analysis category) to color the surface with the grid data.
	You can certainly show the surface(s) with the ligands overlaid.   
You would probably only want to show a few surfaces at most  
simultaneously for understandability (see next answer).
> Given the number of structures, I would much appreciate any advice  
> on how to make this manageable. If Chimera cannot do the  
> calculations, can it import multiple structures saved by another  
> capable software, then overlay them using MultiAlign (including the  
> surfaces)?
	Depending on the speed of your computer, its amount of memory and  
its graphics card, working with 36 structures and their surfaces at  
once may or may not be satisfactory (and unless you have a real high- 
end machine my guess would be not).  You will want to use the Model  
Panel (under Favorites) to control which surfaces/structures are  
being shown -- particularly which surfaces since I imagine that  
looking at more than a few would be incredibly confusing.
	Another thing that will help is to delete parts of structures that  
you aren't interested in.  One trick here is to use MultAlign Viewer  
to select one residue in each structure (create a region by mouse  
dragging that covers one column in the alignment -- those residues  
will be selected), then select the corresponding chains by clicking  
into the main window and hitting the up-arrow key, then right-arrow  
to invert the selection, and finally Actions->Atoms/Bonds->delete to  
delete all atoms that are not part of chains in the alignment.   
Hopefully your ligands will have the same chain ID as the chain in  
the alignment and therefore will not be deleted.  You might want to  
look at your ligands after you've inverted the selection and make  
sure none are selected for the following deletion.  If some are  
selected, deselect them with "~select ligand".
	As a quasi-extreme measure you could prune away parts of the  
structure more than a certain distance from the ligands.  Select the  
ligand clump and use Select->Zone... to select residues further than  
a certain distance from the clump and then delete the selected residues.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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