[chimerax-users] Visualization of the carbon - Cl bond in a small molecule
Elaine Meng
meng at cgl.ucsf.edu
Thu Sep 8 08:46:54 PDT 2022
Hello,
The whole problem is that the spacing in your PDB file is wrong, so all of the chlorine atoms are recognized as carbon. If they were recognized as chlorine in the first place, then you would probably not need to add any bonds because the longer bond length would be recognized.
For the element to be recognized correctly, "Cl" or "CL" in chlorine atom names should be aligned with " C" in carbon atom names (space + C) like this:
ATOM 9281 C1 lig 608 -8.143 -20.714 5.951 1.00 0.00
ATOM 9282 C lig 608 -8.041 -21.112 7.368 1.00 0.00
ATOM 9283 C2 lig 608 -9.902 -22.409 6.096 1.00 0.00
ATOM 9284 C3 lig 608 -11.540 -22.165 7.969 1.00 0.00
ATOM 9285 C4 lig 608 -13.959 -22.401 8.120 1.00 0.00
ATOM 9286 C5 lig 608 -13.859 -23.110 9.294 1.00 0.00
ATOM 9287 C6 lig 608 -12.837 -21.942 7.477 1.00 0.00
ATOM 9288 C7 lig 608 -12.591 -23.333 9.782 1.00 0.00
ATOM 9310 Cl lig 608 -15.581 -22.114 7.491 1.00 0.00
So, if you fix your PDB files to have correct spacing, I think you will also not need to make a bond, change color, etc. since it will happen correctly for the correct element.
See PDB format description
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>>
<https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM <https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM>>
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 8, 2022, at 2:39 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Right, thank you Eric!
> Actually here is the fragment of my ligand directly from the pdb
> ATOM 9281 C1 lig 608 -8.143 -20.714 5.951 1.00 0.00
> ATOM 9282 C lig 608 -8.041 -21.112 7.368 1.00 0.00
> ATOM 9283 C2 lig 608 -9.902 -22.409 6.096 1.00 0.00
> ATOM 9284 C3 lig 608 -11.540 -22.165 7.969 1.00 0.00
> ATOM 9285 C4 lig 608 -13.959 -22.401 8.120 1.00 0.00
> ATOM 9286 C5 lig 608 -13.859 -23.110 9.294 1.00 0.00
> ATOM 9287 C6 lig 608 -12.837 -21.942 7.477 1.00 0.00
> ATOM 9288 C7 lig 608 -12.591 -23.333 9.782 1.00 0.00
> ATOM 9310 Cl lig 608 -15.581 -22.114 7.491 1.00 0.00
>
> so it is defined as Cl and there is no other definition for this atom.
> However, the script can not draw the bond
>
> Il giorno mer 7 set 2022 alle ore 20:15 Eric Pettersen
> <pett at cgl.ucsf.edu> ha scritto:
>>
>> The script is testing against the element symbol of the atom, not the atom name.
>>
>> --Eric
>>
>>> On Sep 7, 2022, at 12:54 AM, Enrico Martinez <jmsstarlight at gmail.com> wrote:
>>>
>>> Great, thanks Eric!
>>> I've just tested your script (opened directly in chimera-X GUI) but it
>>> could not draw a bond ;-)
>>> however the commands changings the representation of the atom Cl works OK!
>>> color :lig at Cl* lime
>>>
>>> P.S. precisely in my system the C atom may be C1, C2 ... C6
>>> and the Cl atom could be either Cl or CL (but I tested with Cl like
>>> was provided in the script :-)
>>> Enrico
>>>
>>> Il giorno mar 6 set 2022 alle ore 19:52 Eric Pettersen
>>> <pett at cgl.ucsf.edu> ha scritto:
>>>
>>>>
>>>> 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
>>>>
>>>>
>>>>
>>>>> 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
>>>>>>>>>
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>>
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