[chimerax-users] Cofactor Morph

[Elaine Meng]

Hi Colin,
There are some tricks/rules as to which atoms get included in the morph, see:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>

"...HET residues such as ligands and ions are only included if at least one of the following applies:

	• the entire atomic models have identical sets of atoms with the same atom names, residue numbers, and chain IDs
	• the "same true" option is used and the HET residues in question are present in all of the input structures with the same atom names, residue names, residue numbers, and chain IDs (even if other atoms are different)
	• the HET residues are bonded to the paired chains either directly or indirectly through other paired HET residues"

You may need to do some hand-editing of PDB files such as to add the cofactor to structures that don't really contain it or bonds to the cofactor that don't really exist (and keep those hidden appropriately so that you aren't showing anything misleading).  If you believe that your set of structures meets these criteria but the cofactor is still not showing up in your morph, however, then you could use Help... Report a Bug and attach a session if you don't mind sharing the data with us.

The simplistic way is to just open an extra structure with the cofactor in it and then selectively make it appear at a certain time using your movie script, but I understand from your question that instead, you need the cofactor itself to change conformation and not simply appear.  Even if you do get it included, the way it morphs may be strange since the method is fairly approximate and does not strive for reasonable sterics at all steps of the morph.  Ways to handle that are to try different interpolation methods or other morphing parameters, or to (manually) construct additional intermediate structures to guide the path that the morphing takes.  These are all imperfect, however, and can be arduous.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jul 27, 2022, at 6:25 AM, Colin Levy via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> From: Colin Levy
> Sent: 27 July 2022 12:58
> To: chimerax-users at cgl.ucsf.edu
> Subject: Cofactor Morph
>  
> Hello, 
> 
> I am new to Chimera X but looking to generate a morph between 4 states of my protein. The protein morph was very simple to achieve but I have been unable to figure out how to include the cofactor in my morph. The cofactor undergoes important rearrangements during the catalysis which I would like to capture in the movie. 
> 
> Thanks in advance, 
> 
> Colin
> 
> Dr. Colin Levy
> c.levy at manchester.ac.uk
> Senior Technical Specialist (XRD)
> Manchester Institute of Biotechnology, Faculty of Science & Engineering
> Tel: +44 (0) 161 306 5168
> The University of Manchester
> 
> <Outlook-ncukp4xa.png>