[Chimera-users] D-Proline modeling in Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 17 16:22:43 PST 2011

As you saw, the bond can't be rotated when it is inside a ring.  You could delete one of the bonds of the ring (probably CD-CG), invert the stereochemistry at CA so it will be a D-proline, change the phi angle to 60, then add the bond back.  At that point the bond might be long and ridiculous, so you could clean it up by minimizing and allowing only the sidechain atoms to move.

Now more details on how to actually do those things in Chimera:

(1) delete CD-CG bond: select that bond with Ctrl-click in the Chimera window, then use Build Structure (under Tools... Structure Editing), Adjust Bonds section, to delete the selected bond.  Or you could use a command, for example (structure 2gbp): ~bond :199 at cd,cg

(2) invert CA: this requires a recent daily build.  You can select the CA with Ctrl-click in the Chimera window, then use Build Structure, Invert section, to invert the stereochemistry.  There is also an invert command which is so new I haven't tried or documented it yet.

(3) change phi angle: you could use Adjust Torsions, or maybe even easier just use the Selection Inspector.  With the CA still selected, click the green magnifying glass near the bottom right corner of the Chimera window to open the Selection Inspector.  In that, inspect "Residue" and change the "phi angle" value to 60.

(4) re-bond CD and CG: you could use a command (e.g. bond :199 at cd,cg ) or select those two atoms and use the Adjust Bonds section of Build Structure.

(5) if the bond looks strained, you can minimize allowing only CB,CG,CD to move: select those three atoms (Ctrl-click on one, Shift-Ctrl-click on other two) and use Minimize Structure (under Tools... Structure Editing) with "Fixed atoms" set to "unselected."  You may want to change "Conjugate gradient steps" to 0 at least the first time you try this, so the calculation won't take as long. There will be some additional dialogs to click through to add hydrogens and assign charges before minimization. If the result still doesn't look "minimized" enough you can run minimization again.

I know this sounds like a lot, but all the steps are really quick except possibly the minimization part.  I just tried the whole process twice on two different structures before sending you this message.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 17, 2011, at 1:15 PM, Raghavender Upadhyayula wrote:

> I am using PyMol for modeling a peptide containing D-aminoacid 
> (D-Proline) residue. I could invert the configuration arounf L-Proline 
> to convert it to D-Proline. But, I want the "Phi" of the Proline to 
> adopt a certain value. When i tried using the torsion command by 
> selecting the bond N-CA of the D-Proline residue, there is no change at 
> all. I want the Phi value to change from -60 deg to +60 deg and use this 
> as the model for further analysis. Also, the "Psi" needs to fixed at 120 
> deg.
> Is it possible in any way to carry out the same steps and achieve the 
> desired results in Chimera.
> Any suggestions on how to carry out this would be highly appreciated.
> -- 
> U.S.Raghavender, PhD
> Postdoctoral Fellow
> SRI International
> 140 Research Drive
> Harrisonburg, VA  22802
> 540.438.6643

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