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

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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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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)

--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

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---------------------------------------------------------------------------------------------

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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