Visualization of the carbon - Cl bond in a small molecule
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@CL1 atoms idatm_type CL show :lig@*
but the bond is still absent. Would it be possible to rebuild it manually? Cheers, Enrico
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@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@CL1 atoms idatm_type CL show :lig@*
but the bond is still absent. Would it be possible to rebuild it manually? Cheers, Enrico
Thank you very much Elaine! Actually I have already tried bond command but it didn't work for this structure: bond :lig@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng meng@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@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@CL1 atoms idatm_type CL show :lig@*
but the bond is still absent. Would it be possible to rebuild it manually? Cheers, Enrico
As mentioned in the help, there is a "reasonable false" option to add bond even if distance seems too long; try that:
bond :lig@C1 :lig@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@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@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng meng@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@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Great, thank you very much! It works! Cheers, Enrico
Il giorno mar 6 set 2022 alle ore 18:26 Elaine Meng meng@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@C1 :lig@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@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@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng meng@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@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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@C1 :lig@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@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@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng meng@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@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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@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@C1 :lig@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@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@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng meng@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@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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 LabOn Sep 6, 2022, at 9:38 AM, Enrico Martinez via ChimeraX-users chimerax-users@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@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@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@C1 :lig@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@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@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng meng@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@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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@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 LabOn Sep 6, 2022, at 9:38 AM, Enrico Martinez via ChimeraX-users chimerax-users@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@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@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@C1 :lig@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@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@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng meng@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@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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@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@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 LabOn Sep 6, 2022, at 9:38 AM, Enrico Martinez via ChimeraX-users chimerax-users@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@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@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@C1 :lig@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@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@C1 :lig@Cl1 > Created 0 bonds > > Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng > meng@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@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@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@cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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.ht... https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html> <https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#... 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@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@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@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@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@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 LabOn Sep 6, 2022, at 9:38 AM, Enrico Martinez via ChimeraX-users chimerax-users@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@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@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@C1 :lig@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@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@C1 :lig@Cl1 >> Created 0 bonds >> >> Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng >> meng@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@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@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@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >
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Thank you very much Elaine! In fact these pdb were produced directly by the tleap module of amber-tools-22 so I used Chimera-X to visualize the results of the model. :-) Enrico
Il giorno gio 8 set 2022 alle ore 17:46 Elaine Meng meng@cgl.ucsf.edu ha scritto:
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.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@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@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@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@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@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 LabOn Sep 6, 2022, at 9:38 AM, Enrico Martinez via ChimeraX-users chimerax-users@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@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@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@C1 :lig@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@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@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng meng@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@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@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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participants (3)
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Elaine Meng -
Enrico Martinez -
Eric Pettersen