Hello,
ok, so I am making it a bit more difficult. I got the first bond to work.
When I try to do the second bond it keeps bonding to the first original
UNL. Is there a way to re-label the second UNL to where there is not an
overlap of O2 names? Or am I going about this wrong? I attached the other
session I am working on.
Also, I am aware the distance between the lysine and O2's is not
necessarily within reasonable, which I will fix later. I am just trying to
get the bond stuff down, I pasted my log as well so you can see what I did.
open C:\Users\Haten\Documents\PEG_project\Pert_PEG_2k_model.pdb format pdb
Summary of feedback from opening
C:\Users\Haten\Documents\PEG_project\Pert_PEG_2k_model.pdb
warnings Start residue of secondary structure not found: HELIX 1 1 PHE A 29
ASP A 31 1 3
Start residue of secondary structure not found: HELIX 2 2 ALA A 88 ASP A 90
1 3
Start residue of secondary structure not found: HELIX 3 3 ASN A 161 GLY A
163 1 3
Start residue of secondary structure not found: HELIX 4 4 SER A 192 SER A
194 1 3
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 10 VAL A
12 0
60 messages similar to the above omitted
Chain information for Pert_PEG_2k_model.pdb
Chain Description
1.1/A No description available
1.2/A No description available
combine #1.1-3 close true modelId #2Remapping chain ID 'A' in
Pert_PEG_2k_model.pdb #1.2 to 'B'
hide #1.4 models
show :65
label :65 atoms offset 0,0,0
delete :65 & H
label :UNL & O atoms
bond :65@NZ :UNL@O2 reasonable falseCreated 1 bond
combine #1.4,2 close model true #3
Invalid "close" argument: Expected true or false (or 1 or 0)
combine #1.4,2 close true modelId #3
show :76
label :76 atoms offset 0,0,0
delete :76 & H
label :UNL & O atoms
bond :76@NZ :UNL@O2 reasonable falseCreated 1 bond
Thank you,
Heather Noriega
PhD-Pharmaceutical Science student
Howard University
heather.noriega@bison.howard.edu
520-203-1883
On Tue, Feb 8, 2022 at 12:38 PM 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@NZ :UNL@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@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@bison.howard.edu 520-203-1883
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