[chimerax-users] bonding Question

Wed Feb 9 13:21:41 PST 2022

Also as previously mentioned, instead of trying to specify the atoms completely on the command line, you can simply select two atoms in the 3D view (ctrl-click, Shift-ctrl-click) and then use command

bond sel reasonable false

They would still have to be in the same model first, however.

Selection:
<https://rbvi.ucsf.edu/chimerax/docs/user/selection.html>

Elaine

> On Feb 9, 2022, at 1:17 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Heather,
> You've added another model, #3 as shown in the Model Panel when you open that session.  I'm not sure exactly what atom you wanted to bond with what, but you can't make a bond between two different models.  If the two atoms you want to bond to each other are in two different models you would have to combine those models into one model first, as in my previous message.
> 
> I didn't know you were going to add more models in your workflow.  If you are going to add more and more copies of UNL then you should just do one big combine at the end to make a single model (and close the originals).  Then, make whatever bonds you want.  It would be too tedious to combine, bond, combine, bond, etc. over and over again for each new model you added.
> 
> There should always be a way to specify atoms uniquely.  I.e. if there is more than one UNL residue then they would have different model numbers and/or chain IDs and you can specify some atom uniqely by # model / chain ID : residue name or number @ atom name.  As I mentioned above, you can't add a bond between two different models, so you would probably have combined them into the same model.  In that case they would have different residue numbers and/or chain IDs.  To review how to specify atoms by model number, chain ID,  residue name or number, and atom name, see:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy>
> 
> I hope this helps,
> Elaine
> 
>> On Feb 9, 2022, at 9:56 AM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> 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
>> 
>> 
>> <heather-result.png>
>> 
>>> 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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>> 
>> <mab_PEG2K_issue.cxs>
> 
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