[Chimera-users] morph & ligands

Hernando J Sosa hernando.sosa at einstein.yu.edu
Mon Sep 18 14:57:58 PDT 2017


Thanks Elaine. I did try making a covalent bond with the bond command between the protein and the ligand (same atoms bonded in the two conformers) but that didn't work; the ligand still disappear in the morph movie. I'll try the examples in the tutorial. 

Best 

H.


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Monday, September 18, 2017 12:17 PM
To: Hernando J Sosa
Cc: chimera List
Subject: Re: [Chimera-users] morph & ligands

Hi Hernando,
While the morph (trajectory) model itself may not include the ligand, it is very common to simply display the ligand(s) from the other, input models.  You would just make sure that the model with the ligand of interest is shown (e.g. with “Shown” checkbox in Model Panel), and then hide all of its other atoms and ribbons that you don’t want to show.

Even fancier, with a little more work you could (A) make the ligand appear only at a certain point in the morph playback instead of the whole time, or (B) make it fly into the binding site. 

There is an example of (A) in the animation gallery.  See the first movie, “kinase morph” and its command script.  The “coordset” command is used to play back the previously calculated morph trajectory model #3.  There are several “coordset” commands to play back different parts of the trajectory, interspersed with commands to show the ligand residue ACP, some sidechains, and 2D labels.
<http://www.rbvi.ucsf.edu/chimera/animations/animations.html#kinase-morph>

There is an example of (B) in this movie-making tutorial:
<http://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html>

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


> On Sep 18, 2017, at 8:30 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> 
> Sorry that was an old question and here was the answer.
> 
> ----------------------------------------------------------
> As I had understood it (and had written in the documentation)
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pairing>:
> 
> "HET residues such as ligands and ions are only included if they are present in both structures and attached to the same atom(s) in the paired chains by at least one "covalent" bond (which can be an unrealistic bond added manually, e.g., with the command bond, and subsequently undisplayed) or ion coordination pseudobond. 
> 
> Once residues are paired, atoms in common within those residues are paired. In paired residues of the same type, atom pairing is straightforward. In paired residues of different types, only atoms with the same names are paired, and only a single connected fragment is kept per residue."
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry University of California, San 
> Francisco
> 
> 
> -----Original Message-----
> From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On 
> Behalf Of Hernando J Sosa
> Sent: Sunday, September 17, 2017 8:00 PM
> To: chimera List
> Subject: [Chimera-users] morph & ligands
> 
> [This sender failed our fraud detection checks and may not be who they 
> appear to be. Learn about spoofing at 
> http://aka.ms/LearnAboutSpoofing]
> 
> Is there a way to  keep & show the ligands in the Morph between structures?.  In the morphs that I've tried the ligands do not show up.
> 
> Thanks
> 
> H.




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