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@cgl.ucsf.edu