[Chimera-users] question

[Eric Pettersen]

On Mar 26, 2004, at 12:32 PM, Wendy Ochoa wrote:

> Could you please tell me how can I define the secondary structure of 
> the protein i am displaying with chimera.
> I know the secondary structure of my pdb, so I would like to draw a 
> picture of the protein showing the B sheets and alpha helix in 
> different colors.

Hi Wendy,
	There are two parts to coloring your secondary structure elements in 
Chimera:  making Chimera aware of where the secondary structure is, and 
then coloring the elements.  Since I'm not sure which part is proving 
to be the stumbling block for you, I'll discuss both.

Getting SS info into Chimera:
	If your PDB file has HELIX and SHEET records then Chimera will honor 
these.  http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_42.html 
discusses the format of HELIX records and 
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_44.html discusses 
SHEETs.  You could create appropriate records in an editor and add them 
to the beginning of your file.  Chimera is a stickler about formatting, 
so you would need to make sure the information is in the correct 
columns.  Comparing against HELIX and SHEET records from a standard PDB 
file is probably the easiest way to do that.  This is likely the best 
approach.
	An alternative is to actually make the assignments in Chimera.  
Chimera will use the 'ksdssp' command to automatically make secondary 
structure assignments to files missing HELIX and SHEET records.  You 
could wipe out these assignments by selecting the whole structure 
(Select->Select All) and use the Selection Inspector's Residue category 
to assign non-helix/non-sheet to everything.  [The Selection Inspector 
can be reached via the button in the lower-right corner of the Chimera 
window.]  Then select the residues you want to assign structure to 
(possibly via the Model Panel's "sequence..." button) and again use the 
Selection Inspector to set the secondary structure type.  You could 
then save a session which would contain the assignments you made.
	With either of the above approaches, you would want to be using the 
latest snapshot release (1.1917) since previous versions don't save 
secondary structure information into session files.

Coloring SS:
	If you want non-helix/non-sheet segments to have a particular color, 
first color the whole structure that color.  Then select helices or 
sheets (Select->Structure->secondary structure->helix or ...->sheet) 
and color those (Actions always operates on the current selection BTW), 
then select and color the other element type.
	The next release will have an entry in the Actions->Color menu for 
coloring all secondary structure elements with separate colors in one 
operation.  So this will be slightly more convenient soon.

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