Hi Damir, Currently Chimera does not include much functionality for peptide building/modeling. However, you can open the two structures from two separate files and move them around relative to each other. There is no advantage in Chimera to putting them in the same structure and forming a bond - either way, it will not predict for you how the two structures may interact. Also, it does not renumber residues or change chain ID's, so you would still have to do those tedious things yourself. Just open the two proteins from separate files (as separate models) and move them around. You can "freeze" one and move just the other using the "Active" checkboxes in the Model Panel (under Favorites). The little boxes under the Command Line and the command "select" can be used to do the same thing. There are also moving commands that only work on the unfrozen model, see "move" "turn" etc. Command index: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html You might want to use Find Clashes/Contacts to monitor bad contacts while you are moving things around. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html I like to use the option to draw pseudobonds (lines) between atoms as they come close together. Whenever you get a configuration or relative position of the two structures that seems reasonable to you, you can write that out into a single PDB file (but still as two models, which will not actually be bonded) or two separate PDB files - make sure to save both of them relative to the same model number. You could even rotate bonds to make it look like one chain connects to the other even though they are really separate, although that might be hard. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#adjust Besides saving PDB files, you can use the "savepos" command to save the positions, and then you also need to save a session with the positions in it. When a position has been saved, you can use "reset" to immediately restore it, or restore it gradually in a specified number of frames from the current position (which might be fun in a movie). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 26, 2007, at 2:24 PM, Damir Perisa wrote:
hi all, maybe this is a little bit too far over the capabilities of chimera, but i hope somebody can help me or give input.
i would like to connect two PDB structures into one chain of aminoacids. one PDB is from one globular domain, the other is from another globular domain including linker. i would like to try to put them together and see how (what possible conformations) they fit together. what orientations are possible and how it would look like (visualisation, making movies, convincing non-scientists, ...).
i could edit the PDB files in a text editor, but i would not want to calculate the cordinates by hand first - are there no tools to glue together chains?
thanx for any input how to do this with chimera or any other programme, best regards, Damir