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

[André]

Hi Christian,

Thank you so much for your solution! That indeed helps a lot, since it
shows me how to execute ChimeraX scripts independently and directly from
Python!

Now, do you know which commands I should use to calculate the following
structural attributes for all residues: areaSAS, areaSES, relSESA, bfactor,
kdhydro, phi, psi?

I do it manually in Chimera (haven't figured out how to do the same in
ChimeraX yet), by following the route: Tools -> Structure Analysis ->
Render by Attribute -> File -> Save Attributes -> Attribute to Save, which
allows each attribute of residues to be saved as txt files, which contain
the residue number and respective attribute, for all residues in the
protein. For example, the file for areaSAS looks like this:

attribute: areaSAS
recipient: residues
:1.B 116.71626508235931
:2.B 118.39353680610657
...

Thus, that's what I wanted to do: figure out which commands I should use to
get the same result as the manual route above (although it  is not really
necessary that the txt file is generated directly -- if the needed
information appear in the stdout_as_str string, just like in the example
you showed, I'd be able to parse it to a file, and the problem would be
solved!).

Once again, thank you for your help!

Best,
André.



Em sex., 21 de jan. de 2022 às 09:56, Christian Tüting <
christian.tueting at biochemtech.uni-halle.de> escreveu:

> Hi André,
>
> i am pretty sure, that my solution is very crude and that there are
> better ways of doing it (like importing chimerax in the python code
> directly). I guess, you'll get more anwsers soon.
>
> I quickly wrote a script, which performs a chimerax task independently,
> by just running python code.
>
> First: a chimerax script file with the desired commands:
>
> script.cxc:
> open 7ott
> surface #1
> mearuse area #1
> exit
>
> Note: the exit command is needed, otherwise the subprocress will idle in
> the chimerax cmd line.
>
>
> Second: a python script, which execute this script in chimerax and
> fetches the output:
>
> test.py:
>
> import subprocess
> import os
>
> cwd = os.getcwd()
>
> chimerax = "/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX"
> scriptfile = f"{cwd}/script.cxc"
>
> cmd = [chimerax, "--nogui",scriptfile]
> p = subprocess.run(" ".join(cmd),shell = True,capture_output=True)
>
> stdout_as_str = p.stdout.decode("utf-8")
> print(stdout_as_str)
>
> This just runs a subprocess and fetches the output to a string, which
> you can than further analyse.
>
>
> Best
> Christian
>
>
>
> Dr. rer. nat. Christian Tüting
>
> Kastritis Laboratory for Biomolecular Research
> Cryo-Electron Microscopy & Computational Structural Biology
> ________________________________________________
> Martin-Luther-Universität Halle-Wittenberg
> Biozentrum, Room A.2.19
> IWE ZIK HALOmem NWG III
> "Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
> Weinbergweg 22, 06120 Halle
> tel: +49 345 5524985
> web (Lab): https://blogs.urz.uni-halle.de/kastritislab/
> web (HALOmem): https://www.halomem.de/en/
> >>> André via ChimeraX-users <chimerax-users at cgl.ucsf.edu> 01/21/22 1:29
> PM >>>
> 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 the files are exported manually, and, for the purpose
> of
> building a fully automated pipeline, it would be great to also automate
> this step of calculating the attributes and exporting their respective
> files.
>
> I searched a lot, and tried some ways to achieve such an automation
> (using
> Chimera), but nothing worked.
> And I also considered using ChimeraX. In particular, I went through
> ChimeraX Programming Manual (
> https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html#), but, if I
> understood correctly, I'd only be able to import chimerax and use its
> functions in the Python interpreter within ChimeraX (Tools >> General >>
> Shell).
> At first, I'd like to import chimerax as a module in a Python
> interpreter
> outside of ChimeraX, so that manually opening ChimeraX wouldn't be
> necessary in order to save the files with the residues' attributes. But,
> from some other threads in the mailing list, I found that it wouldn't be
> possible (right?)
>
> But I also found out that I could write a .py script which calculates
> and
> exports the files with the residues' properties, and then run it with
> ChimeraX application from the command-line, something like: *chimerax
> --nogui myscript.py*
> If that works, I think that my automation problem would be solved! The
> only
> problem is that I really couldn't figure out the Python code to
> calculate
> and export the aforementioned residues' properties (I took a look in
> ChimeraX Recipes (https://rbvi.github.io/chimerax-recipes/), but I
> couldn't
> find what I need, nor more detailed documentation).
>
> Given that, I'd like to know if anyone has done something like this,
> and/or
> have any guidance on how I could proceed.
>
> I really appreciate any help you can provide!
> (And thanks to Tom Goddard for suggesting moving the discussion here to
> the
> ChimeraX mailing list).
>
> Thank you so much,
> André.
>
>
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