Python script to add hydrogens to selected carbon atoms
Dear developers, I am trying to automatize a task using the chimera python interface. In the graphical user interface, I can get the result I want by performing the following actions: 1) Select a carbon atom (ctrl+left button) 2) Tools --> Structure Editing --> Build Structure 3) In the "Build Structure" window, select "Modify Structure" 4) Change selected atom to...: "Element C", "Bonds 4", "Geometry Tetrahedral" (basically the default) 5) Apply 6) Save as pdb Is it possible to create a python script to do 1-6 (repeating 1-5 for several carbon atoms identified by residue id and name)? I could then very easily prepare a bash script to apply these changes to hundreds of pdb files. I tried asking chatGPT for a quick answer, but most probably it is using python classes and methods that actually do not exist. Looking at the online documentation was also unsuccesful, but maybe you could point me to the right place. Thanks a lot! Best, Davide Dr Davide Mandelli Institute of Neuroscience and Medicine INM-9 Forschungszentrum Jülich Email: d.mandelli@fz-juelich.de<mailto:m.alfonso-prieto@fz-juelich.de> --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens --------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------
Hi Davide, I should mention that this whole process would have been easier in ChimeraX because there are command equivalents for all these operations, and as you use a tool (like Build Structure) the equivalent commands are shown in the log. Nonetheless, here is some example code for doing this in Chimera. I am going to assume that you have the chain ID in a variable named 'chain_id', the residue number in 'res_num', and the atom name in 'a_name'... from chimera import MolResId, Molecule mol = chimera.openModels.list(modelTypes=[Molecule])[0] r = mol.findResidue(MolResId(chain_id, res_num)) a = r.atomsMap[a_name][0] from BuildStructure import changeAtom changeAtom(a, 'C', 4, 4, name=a.name) Then you can save as a PDB file using runCommand() to run the appropriate command (see Very Basic Chimera Programming Primer <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>) --Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 18, 2024, at 3:04 AM, Mandelli, Davide via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear developers,
I am trying to automatize a task using the chimera python interface.
In the graphical user interface, I can get the result I want by performing the following actions:
1) Select a carbon atom (ctrl+left button) 2) Tools --> Structure Editing --> Build Structure 3) In the "Build Structure" window, select "Modify Structure" 4) Change selected atom to...: "Element C", "Bonds 4", "Geometry Tetrahedral" (basically the default) 5) Apply 6) Save as pdb
Is it possible to create a python script to do 1-6 (repeating 1-5 for several carbon atoms identified by residue id and name)?
I could then very easily prepare a bash script to apply these changes to hundreds of pdb files.
I tried asking chatGPT for a quick answer, but most probably it is using python classes and methods that actually do not exist. Looking at the online documentation was also unsuccesful, but maybe you could point me to the right place.
Thanks a lot!
Best, Davide
Dr Davide Mandelli
Institute of Neuroscience and Medicine INM-9 Forschungszentrum Jülich Email: d.mandelli@fz-juelich.de <mailto:m.alfonso-prieto@fz-juelich.de>
--------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens --------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------
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Dear Eric, Thanks a lot! Best, Davide Dr Davide Mandelli Institute of Neuroscience and Medicine INM-9 Forschungszentrum Jülich Email: d.mandelli@fz-juelich.de<mailto:m.alfonso-prieto@fz-juelich.de> --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- ________________________________ Da: Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu> Inviato: giovedì 19 settembre 2024 00:00:50 A: Mandelli, Davide Cc: chimera-users@cgl.ucsf.edu Oggetto: [Chimera-users] Re: Python script to add hydrogens to selected carbon atoms Hi Davide, I should mention that this whole process would have been easier in ChimeraX because there are command equivalents for all these operations, and as you use a tool (like Build Structure) the equivalent commands are shown in the log. Nonetheless, here is some example code for doing this in Chimera. I am going to assume that you have the chain ID in a variable named 'chain_id', the residue number in 'res_num', and the atom name in 'a_name'... from chimera import MolResId, Molecule mol = chimera.openModels.list(modelTypes=[Molecule])[0] r = mol.findResidue(MolResId(chain_id, res_num)) a = r.atomsMap[a_name][0] from BuildStructure import changeAtom changeAtom(a, 'C', 4, 4, name=a.name) Then you can save as a PDB file using runCommand() to run the appropriate command (see Very Basic Chimera Programming Primer<https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>) --Eric Eric Pettersen UCSF Computer Graphics Lab On Sep 18, 2024, at 3:04 AM, Mandelli, Davide via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: Dear developers, I am trying to automatize a task using the chimera python interface. In the graphical user interface, I can get the result I want by performing the following actions: 1) Select a carbon atom (ctrl+left button) 2) Tools --> Structure Editing --> Build Structure 3) In the "Build Structure" window, select "Modify Structure" 4) Change selected atom to...: "Element C", "Bonds 4", "Geometry Tetrahedral" (basically the default) 5) Apply 6) Save as pdb Is it possible to create a python script to do 1-6 (repeating 1-5 for several carbon atoms identified by residue id and name)? I could then very easily prepare a bash script to apply these changes to hundreds of pdb files. I tried asking chatGPT for a quick answer, but most probably it is using python classes and methods that actually do not exist. Looking at the online documentation was also unsuccesful, but maybe you could point me to the right place. Thanks a lot! Best, Davide Dr Davide Mandelli Institute of Neuroscience and Medicine INM-9 Forschungszentrum Jülich Email: d.mandelli@fz-juelich.de<mailto:m.alfonso-prieto@fz-juelich.de> --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu<mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
participants (2)
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Eric Pettersen -
Mandelli, Davide