[chimerax-users] bonding Question

[Elaine Meng]

Hi Heather,
You want to make a bond between two atoms, but your specification includes the whole lysine, which has multiple atoms.  Secondly, the bond can only be made between atoms that are in the same model.  Your session has 3 models #1.1,1.2,1.3 even though they are all grouped as #1. You would need to at least combine the two you want to bond to each other, but this example command combines all three to make a new model #2 and closes the originals:

combine #1.1-3 close true model #2

(actually there is still a "grouping model" #1 open according to the Model Panel, but its presence is a bug and you could ignore it)

"combine" help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>

Next, you have to choose which two atoms in this new model #2 you want to bond.  Show the lysine atoms and label them:

show :76
lab :76 atoms offset 0,0,0

...since the lysine has hydrogens filling all the bond vacancies you would probably want to delete a hydrogen from whichever atom will be forming the bond, or else it would have too many bonds.  E.g. to delete all hydrogens from the lysine (you could add hydrogens back after forming the bond, using "addh")l:

delete :76 & H

Similarly I don't know if forming a bond to O2 in your polymer is chemically reasonable.  Label polymer oxygens:

lab :UNL & O atoms

I don't know if any of the oxygens is within reasonable bonding distance of the lysine, either.  However, setting aside the issue of whether it makes any sense chemically, if you wanted an NZ-O2 bond, it could be command

bond :76 at NZ :UNL at O2 reasonable false

... then it looks like the attached image

Colon (:) indicates residue name or number, and @ symbol indicates atom name.  I have also used element symbols above (which don't have the @). See the "atom specification" help
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

Or if you don't want to figure out atom and residue names, you could just select the two atoms (Ctrl-click, Shift-Ctrl-click) and then use command

bond sel reasonable false

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



> On Feb 8, 2022, at 7:43 AM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> I hope you are well. I have a quick question about the bond command. I attached the pdb file I have been using to try and learn this command. I am having a hard time figuring out how I should write it on the command line. If I want to create a bond between residue Lys76 from the antibody and the Oxygen #2 from my polymer, how would I write it on the command line?
> 
> bond :lys76:O2
> 
> I have read the section in the manual but I think I am misunderstanding something, it keeps giving me a mangled atom specifier. 
> 
> Also, I figured out the problem from my last question/email about the volume in my viral capsid. :) Thank you for your help on that one Elaine. 
> 
> 
> Thank you,
> 
> Heather Noriega
> PhD-Pharmaceutical Science student 
> Howard University
> heather.noriega at bison.howard.edu
> 520-203-1883
> <TEST_mAB_poly.pdb>_______________________________________________
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