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

[André]

Hi all,

Christian, thank you so much for your answer! I considered using biopython,
but, as you pointed out, I also couldn't find a way to calculate SESA
(areaSES), which is why I switched to Chimera, which allows such a
calculation.
As Elaine explained, SESA is the solvent-excluded surface aerea, and the
diagram she referenced is quite useful to understand their difference. As
far as I could find out, there's not an immediate way to get SESA from SASA
--- a specific algorithm is used to do so. I still think that I'll be able
to run Chimera from python in the --nogui mode, so that it won't be
necessary to implement such an algorithm, But, if I do, I'll post it here.

Elaine and Christian, thank you again for your replies and valuable help!

Best,
André.

Em seg., 24 de jan. de 2022 às 13:42, Elaine Meng <meng at cgl.ucsf.edu>
escreveu:

> Hi Christian,
> Just FYI and for the others on the list...
>
> People would like to have a lookup table of  "completely exposed"
> reference values for SAS (not SES) for each of the standard amino acids
> because that is the only type of area that can be calculated in ChimeraX.
>  ChimeraX calculates the residue SAS in the context of the specific
> structure, and then if there were a reference "completely exposed" value,
> you would divide by that to get % exposed.  It's just a normalization
> factor for the size of the residue.
>
> We already have reference values for SES (which could be used in Chimera
> because Chimera can calculate SES).  We just don't have them for SAS.
>
> There is a diagram showing the difference between SAS and SES here:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jan 24, 2022, at 4:28 AM, Christian Tüting via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hi Andre,
> >
> > I checked what you want to calculate. For me, I didn't  even know that
> > there is something called SES, I only worked with SAS(A)  so far. As far
> > as I see, you need a reference for the SES, to calculate  the relative
> > exposure?
> >
> > But for the rest, I think you can go for a  python only solution, which
> > is way faster, than starting chimera(x) for  each calculation:
> >
> > dihedrals: calculatable from coordinates (so from pdb)
> > bfactor: directly in pdb file
> > kdh: value based on residue type (also in pdb)
> > sasa: calculatable from coordinates
> >
> >
> > So I wrote a piece of code, which will calculate these from a input pdb
> > file and save the values in a dataframe.
> > Here is the code: https://paste.ofcode.org/gCH5HDVtkg4DD3fcdqKfRZ (link
> > will be expire in 1 week).
> >
> > I also attach the file to this mail.
> >
> > The code was tested for the pdb file 1trn (hardcoded in the file), which
> > contains mutliple chains and heteroatoms and unusual residues, and as
> > far as I can see, the results looks correct. In principle, it's a
> > function, which just need to full path to the pdb file.
> >
> >
> > For the dependencies, it uses pandas and biopython.
> >
> > Additionally:
> >
> > For the SES calculation, if this could be calculated from the reference
> > and the SASA, it should be easy to implement. If you have a reference
> > for this, I might also include this for you.
> >
> > Best
> > Christian
> >
> >
> > ps. the code is not optimized, e.g., the load pdb module from biopython
> > is used twice. So the code could be also furhter optimized to be faster.
> > Also the manually read-in of the pdb file could be most likely done by
> > biopython and not manually, like I did :D
> >
> >
> >>>> André <andre.jfmdm at gmail.com> 01/21/22 7:06 PM >>>
> > Hi Elaine,
> >
> > Thank you so much for your very helpful answer!
> >
> > Yeah, Tom told me before that it wouldn't be possible to directly
> > calculate
> > SESA and relSESA with ChimeraX. So, I'll probably have to stick with
> > Chimera. I've just discovered the "list" command (functional in
> > Chimera),
> > and I think that with it I'll be able to easily get all the attributes
> > by
> > using the --nogui startup.
> > I'll work on it in the following days, then I'll come back with updates.
> >
> > Once again, thank you very much!
> >
> > Best,
> > André.
> >
> > Em sex., 21 de jan. de 2022 às 13:55, Elaine Meng <meng at cgl.ucsf.edu>
> > escreveu:
> >
> >> Hi André,
> >> Although it displays an SES, ChimeraX does not calculate SES areas,
> > only
> >> SAS areas (command "measure sasa" which also assigns a residue
> > attribute).
> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>
> >>
> >> For Chimera, another group had provided SES reference areas for the
> >> exposed state represented by G-X-G tripeptides, but I don't know of a
> >> similar SAS reference area set for ChimeraX that could be used to
> > calculate
> >> relative exposure, sorry.  In case others are interested, the Chimera
> >> relative exposure calculation giving relSESA is described here:
> >> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html>
> >>
> >> So depending on the importance of SESA and relSESA, you may need to
> > use
> >> Chimera, or at least some method outside of ChimeraX.
> >>
> >> In both ChimeraX and Chimera, bfactor is read from the input PDB file,
> > and
> >> phi and psi are calculated automatically for peptide/protein
> > structures
> >> when they are read in.  ChimeraX atom and residue attributes:
> >> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#atom>
> >> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>
> >>
> >> kdHydrophobicity is not a calculation, but a simple lookup table by
> > amino
> >> acid type.  You may not need either program to "calculate" it, but it
> > is
> >> automatically assigned in Chimera.  It can be assigned in ChimeraX by
> >> running this comand script:
> >> <
> >>
> >
> https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc
> >>>
> >>
> >> ...or you can just assign it directly yourself by lookup table.  The
> >> values along with some alternative hydrophobicity scales (lookup
> > tables)
> >> are summarized here:
> >>
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
> >>
> >> I h> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>
> >>> On Jan 21, 2022, at 7:28 AM, André via ChimeraX-users <
> >> chimerax-users at cgl.ucsf.edu> wrote:
> >>>
> >>> 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, f> > 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.
> >>>
> >>> _______________________________________________
> >>> ChimeraX-users mailing list
> >>> ChimeraX-users at cgl.ucsf.edu
> >>> Manage subscription:
> >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> >>
> >>
> >
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