[chimerax-users] bonding Question

Wed Feb 9 09:56:57 PST 2022

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 at NZ :UNL at 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 at NZ :UNL at O2 reasonable falseCreated 1 bond

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
Howard University
heather.noriega at bison.howard.edu
520-203-1883

On Tue, Feb 8, 2022 at 12:38 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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>
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