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

Thu Feb 3 00:33:04 PST 2022

Hi All,

Andre and I continued this conversation in private, as this was not
Chimera related anymore.

Somehow, we have a question regarding the calculation of the of the SES
and SAS. 

In principle, I looked into the calcsurf.py file in the chimera folder,
and figured out, that this calculation is done by msms with a probe
radius of 1.4 and a density of 2 and noh. So I copied the code into my
workflow and tested this with a xyzr file, generated by the pdb_to_xyzr
shell script from msms, and got the same results, as if I am running
directly msms from command line. So far not suprisingly.

But when we take the same pdb file, the msms code itself gives slightly
different values than chimera. Often, it's not siginificant, but Andre
benchmarked this, and sometimes the difference is more than 1.2 fold.

So this let us come to the conclusion, that chimera somehow calculates a
different xyzr file, compared to what the shell script is doing. I was
not able to find the code for caluclating the xyzr file. Another
explanation is, that chimera treats the results a bit differently. msms
results ses and sas per atom, we "just" summed them per residue to get
the per residue value. But I don't think, that this is done differently
here.

So our questions are:
(a) is the radius definition different in chimera from what is given
with the msms software ( https://ccsb.scripps.edu/msms/downloads/; there
is a shellscript and, more importantly a text file, which defines the
radius of each atom, with a lot of special cases ).
(b) is the structure somehow "filtered" prior to surface calculation.
E.g. are waters, ions, ligands considered part of the structure, of are
they excluded, as this might introduce also some differences
(c) or can you help us find the actual code for this in chimera, than I
will be able to anwser the question myself

Thanks in advance.

Christian

>>> 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> values along with some alternative hydrophobicity scales (lookup
tables)
> are summarized here:
>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> 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> > 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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