[Chimera-users] building linker peptide

[Elaine Meng]

Dear Fabian,
You can add the final bond with the "Build Structure" tool (under  
Tools... Structure Editing) or the command "bond":
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#addbond
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html

You may want to rotate torsions to get the ends closer together before  
adding the bond:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#adjust

You may already know about the "Minimize Structure" tool and  
"minimize" command.  You can allow only parts of the structure to move  
during minimization.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html

However, this process will not likely generate a high-quality model,  
as minimization only goes so far in removing strain and will not cross  
barriers to find more likely conformations.  It may suffice if you are  
aware (and don't mind) that it is a rough model, or you may use the  
structure as a starting point for MD or MC simulations with another  
program.  Alternatively, you could look into other approaches to  
building the linker.  A few programs that might do that are Modeller,  
MolIDE, RAPPER:
http://salilab.org/modeller/index.html
http://dunbrack.fccc.edu/molide/molide.php
http://mordred.bioc.cam.ac.uk/~rapper/
(I haven't tried to use any of these for de novo loop building,  
however).

I should also mention that "addaa", unlike "swapaa", currently doesn't  
use rotamer libraries, so it may not give the best sidechain  
conformations.

There is a little more discussion about Chimera and protein modeling  
in this post:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-January/002202.html

Best,
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 May 18, 2008, at 4:20 AM, Fabian Gmail wrote:

> Dear Chimera experts,
> I am willing to build a peptide "linker" connecting two different pdb
> chains, that is to connect two existing pdb chains with a new peptide
> chain, and if possible minimize it. Is it possible to do that wich
> chimera? I know the command addaa, but to my best understanding this
> command it's not able to connect the end of the new peptide with the
> beginning of the second chain.
>
> Any suggestions will be greatly appreciated.
> Best regards and thanks a lot in advance,
> Fabian