[Chimera-users] Automate calculation and saving of residues' structural attributes

Tom Goddard goddard at sonic.net
Thu Jan 20 19:35:52 PST 2022

Hi Andre,

  Solvent accessible area calculation is prone to failure in Chimera because the Chimera molecular surface code often fails for large structures (e.g. more than 10000 atoms).  ChimeraX has a 100% reliable calculation of solvent accessible area and surfaces.  But ChimeraX does not compute solvent excluded area, although you could get that from the surface calculations in ChimeraX I guess.

  I work on ChimeraX and could help with Python code to export values.  Some examples of ChimeraX Python code are here


If you want to use ChimeraX, let's discuss on the ChimeraX mailing list chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>.


> On Jan 20, 2022, at 7:27 PM, André via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello!
> I'm working on an automated pipeline (in Python) for the structural analysis of proteins. In particular, I'm using Chimera to calculate and save to .txt files some structural properties of residues (namely: areaSAS, areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the inputs of the pipeline.
> However, currently these files are exported manually, and, for the purpose of building a fully automated pipeline, it would be great to also automate this step of generating the attributes and exporting their respective .txt files.
> I searched a lot, and tried some ways to achieve such an automation, but nothing worked (if you'd like to know about these (unsuccessful) ideas that I had, I can share them in next messages).
> Given that, I'd like to know if anyone has done something like this, and/or have any guidance on how I could proceed, if that's something possible at all to be done with Chimera (or even ChimeraX).
> I really appreciate any help you can provide!
> Thank you so much,
> André.
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