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

André andre.jfmdm at gmail.com
Fri Jan 21 03:51:37 PST 2022

Hi Tom,

Oh, I see! Sure, I'm definitely willing to use ChimeraX, given what you
said. I'll send the e-mail to the ChimeraX mailing list, so we can discuss
it there.

Thank you so much for your reply!


Em sex., 21 de jan. de 2022 às 00:35, Tom Goddard <goddard at sonic.net>

> 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
> https://rbvi.github.io/chimerax-recipes/
> If you want to use ChimeraX, let's discuss on the ChimeraX mailing list
> chimerax-users at cgl.ucsf.edu.
> Tom
> 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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