[Chimera-users] how to "connect" two proteins

[Elaine Meng]

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 at 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