[chimerax-users] Visualization of the carbon - Cl bond in a small molecule

[Eric Pettersen]

Hi Enrico,
	I have attached a Python file that will look for chlorines with no bonds and bond them to the nearest carbon in the same structure.  You run it with the command "open (wherever you saved the file)/bond_cl.py".

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

-------------- next part --------------
A non-text attachment was scrubbed...
Name: bond_cl.py
Type: text/x-python-script
Size: 530 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220906/12888826/attachment.bin>
-------------- next part --------------


> On Sep 6, 2022, at 9:38 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> P.S Assuming that I am running chimeraX from batch file, would it be
> possible to script it a little bit to create the bond with the Cl1 and
> the nearest carbon atom of the ligand (it may be C1, C2, C3, C4 etc
> ..) ?
> Many thanks in advance
> Enrico
> 
> Il giorno mar 6 set 2022 alle ore 18:33 Enrico Martinez
> <jmsstarlight at gmail.com> ha scritto:
>> 
>> Great, thank you very much!
>> It works!
>> Cheers,
>> Enrico
>> 
>> Il giorno mar 6 set 2022 alle ore 18:26 Elaine Meng
>> <meng at cgl.ucsf.edu> ha scritto:
>>> 
>>> As mentioned in the help, there is a "reasonable false" option to add bond even if distance seems too long; try that:
>>> 
>>> bond :lig at C1 :lig at Cl1 reasonable false
>>> 
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
>>> 
>>>> On Sep 6, 2022, at 9:22 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Thank you very much Elaine!
>>>> Actually I have already tried bond command but it didn't work for this
>>>> structure:
>>>> bond :lig at C1 :lig at Cl1
>>>> Created 0 bonds
>>>> 
>>>> Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng
>>>> <meng at cgl.ucsf.edu> ha scritto:
>>>>> 
>>>>> Hello,
>>>>> Maybe the distance was longer than what ChimeraX thinks is a bond.  Anyway, if the bond is missing you can add it with the "bond" command (or if you prefer GUI, with Tools... Structure Editing... Build Structure tool, Adjust Bonds section).
>>>>> 
>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.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 6, 2022, at 8:34 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>>>>> 
>>>>>> Dear ChimeraX users!
>>>>>> I have an issue with the visualization of the small molecule obtained
>>>>>> from the tleap module of the amber tools. First of all in vmd and
>>>>>> pymol everything looks OK. In the ChimeraX there is no bond between
>>>>>> atom CL of the ligand and the aromatic C atom. I've tried to change
>>>>>> atom type for the CL:
>>>>>> setattr :lig at CL1 atoms idatm_type CL
>>>>>> show :lig@*
>>>>>> 
>>>>>> but the bond is still absent. Would it be possible to rebuild it manually?
>>>>>> Cheers,
>>>>>> Enrico
>>>>> 
>>>> _______________________________________________
>>>> ChimeraX-users mailing list
>>>> ChimeraX-users at cgl.ucsf.edu
>>>> Manage subscription:
>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>>> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users