[chimerax-users] 2D plots and graphs for protein-ligand interactions

Fri Sep 9 01:07:46 PDT 2022

Thank you Tom!
Actually I faced the problem with the installation of the chimerax-daily on
the ubuntu-20.04
(currently I am using the 1.4 version realized in june 2022). Here is the
error of the installation:

root at Perfetto-7920-Tower:/home/enrico/Downloads# dpkg -i
./chimerax-daily.deb
(Reading database ... 322925 files and directories currently installed.)
Preparing to unpack ./chimerax-daily.deb ...
Deregister desktop menu and associated mime types
Remove Python cache files
Unpacking ucsf-chimerax-daily (2022.09.08ubuntu20.04) over
(2022.09.08ubuntu20.04) ...
Setting up ucsf-chimerax-daily (2022.09.08ubuntu20.04) ...
Install desktop menu and associated mime types
Traceback (most recent call last):
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py",
line 724, in init
    run(sess, cmd)
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py",
line 38, in run
    results = command.run(text, log=log, return_json=return_json)
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py",
line 2897, in run
    result = ci.function(session, **kw_args)
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/cmd.py",
line 23, in linux_xdg_install
    install(session, verbose=verbose, system=system)
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py",
line 428, in install
    generate(session, info, system, verbose)
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py",
line 421, in generate
    from chimerax.core import localized_app_name
ImportError: cannot import name 'localized_app_name' from 'chimerax.core'
(/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__init__.py)
dpkg: error processing package ucsf-chimerax-daily (--install):
 installed ucsf-chimerax-daily package post-installation script subprocess
returned error exit status 70
Processing triggers for man-db (2.9.1-1) ...
Errors were encountered while processing:
 ucsf-chimerax-daily

Il giorno ven 9 set 2022 alle ore 00:07 Tom Goddard <goddard at sonic.net> ha
scritto:

> Hi Enrico,
>
>   As Elaine says, ChimeraX isn't a plotting package, so it doesn't let you
> set colors, sizes, scales, ..., of plots.  You could save the plot ChimeraX
> makes with Python, but I don't think it is very useful to do in an
> automated way because the aspect ratio of the plot will probably be poor
> and you cannot control it in a script.  At any rate, for reference here is
> Python that would save the image
>
> from chimerax.core.commands import run
> plot = run(session, 'crosslinks histo #1.1')
> plot.save_plot('histogram.png')
>
> This will need a September 9, 2022 or newer daily build because I just
> made the "crosslinks histogram" command return the plot, before it did not
> return it.
>
>   The figures in the paper were made interactively in ChimeraX on a high
> resolution display and just a screen capture was used to save an image.
> Although as Elaine notes the right-click context menu on those plot windows
> has a "Save Plot As..." menu entry that will save at 300 dots per inch
> resolution.
>
> Tom
>
> Example histogram of hydrogen bond lengths for pdb 7qfc saved with the
> context menu entry "Save Plot As..."
>
>
> On Sep 8, 2022, at 9:10 AM, Elaine Meng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hello,
> The main advantage of these plots inside ChimeraX is that they are
> interactive with the 3D structure (e.g. you click something on the plot, it
> does something in the 3D window).  They weren't meant for making figures
> for hundreds of molecules in scripts.
>
> So, there are no options to customize plot appearance, and the only way to
> save the histogram currently is by interactively using the context menu on
> that window, as mentioned in the help:
> <
> https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram
> >
>
> If you wanted to make your own plots with everything about the appearance
> customized, currently you would have to write python scripts to dump the
> data and then use your own favorite plotting program to generate images.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Sep 8, 2022, at 1:40 AM, Enrico Martinez via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Thanks a lot, Elaine!
> Actually crosslink hist #1 works very well!
> Could you please specify would it be possible to plot the histogram
> (using batch chimera-x execution) or alternatively add it directly to
> the produced png image?
> I did not find any possibility to save the plot or to customize its
> appearance (color of the bars etc).
> Cheers
> Enrico
>
> Il giorno mer 7 set 2022 alle ore 17:52 Elaine Meng
> <meng at cgl.ucsf.edu> ha scritto:
>
>
> Hello!
> The chain contacts diagram shown in Fig 4b is made with the "interfaces"
> command.  Then you can use context menu on that contacts diagram to make
> the interface-residue plot in Fig 4d.  Please see the "interfaces" help for
> details on both of those.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>
>
> The histogram plot in Fig 5b  is made with the command "crosslinks
> histogram" but first you have to have some crosslinks, or other pseudobonds
> such as from finding H-bonds or contacts.  Then in the "crosslinks
> histogram" command you specify the pseudobond model to plot their
> distances.  See "crosslinks histogram" help:
> <
> https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram
> >
>
> Also for a more detailed example see the "Interactive H-bond Histogram"
> feature highlight, which includes a script (.cxc file):
> <https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Sep 7, 2022, at 2:18 AM, Enrico Martinez via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear ChimeraX users!
> I am dealing with the analysis of protein-ligand interactions in a
> single PDB structure. I am looking for any tools implemented in
> Chimera-X, which could be used to analyse the interactions (besides
> the hbond and contact tools giving info in the log files).
> I wonder to know which commands and corresponded ChimeraX tools could
> be used to produce the 2D contact diagrams shown on the Fig.4 as well
> as python graphs demonstrated on the Fig.5 in the Chimera-X article:
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/
>
> Many thanks in advance!
> Cheers
> Enrico
>
>
>
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