[Chimera-users] Reaction Mechanism Movie

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 7 14:30:56 PDT 2014

On Apr 5, 2014, at 1:06 PM, Moses Adenaike wrote:

> Dear Dr. Pettersen,
>    I am wondering how I would go about making a moive detailing a biochemical reaction. For example, I want to show a DNA polymerase reaction, essentially a ligation between the backbone of two nucleotides. How would I go about doing so? I know chimera has a make new bond function but I haven't been too successful at getting that to work. 

Hi Moses,
	It is typically better to send questions like this to the chimera-users mailing list than to me directly so that others can benefit from the answer and in case others on the list have more expertise on the topic than I do.
	The simplest method is to decide which frame# you want the bond to start existing and use the "Define script…" entry in MD Movie's Per-Frame menu to define a one-command script to execute at that frame.  For example, if you wanted a bond between :337.A at P and :338.A at O3' to exist starting with frame 53, in the Per-Frame dialog you would set "Interpret script as" to "Chimera commands" and enter as your script:

#53 bond :337.A at P :338.A at O3'

	There is also a hidden capability in Chimera to compute all bonds on a per-frame basis.  I can tell you how to access that if it turns out you really need it.
	However, for the purpose of making a movie it might be nice to have a more "continuous" representation of the bond forming than just the binary on/off that the above approaches give you.  I have attached a Python script that you can use the Per-Frame dialog (with "Interpret script as" set to Python, and reading in the script with the "Insert text file…" button) to have a bond form (by starting out very thin and becoming thicker) as two designated atoms approach each other.  There are some values at the top of the script that you can edit to make it work best in your situation.  There is a distance value for when the bond begins to exist (noBond, default 3.5) and when it reaches full size (fullBond, default 2.0).  There is a two-member list of residue IDs (resIDs) for the atoms involved in the bond, and a list of atom names (atomNames).  Let me know if you need more help than this.
	Hmmm, this all assumes you have a trajectory of the reaction.  You may have to use the Morph Conformations tool to create such a trajectory if you don't have one already.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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