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

Fri Sep 9 01:09:04 PDT 2022

P.S. Are there other possibilities to install chimera-daily in a distinct
directory from the chimerax stable release not to overlap between the both ?

Il giorno ven 9 set 2022 alle ore 10:07 Enrico Martinez <
jmsstarlight at gmail.com> ha scritto:

> 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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>>
>>
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