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  <div class=""><p class="">So the chimerax-daily command is installed in a separate location
      from the production releases.  So if you install both, you will
      have a /usr/bin/chimerax and a /usr/bin/chimerax-daily.</p><p class="">The bug in the installation process was in the post-install
      script, so the command is already there.  That particular bug has
      to with with integrating ChimeraX in the system menus and no
      effect on starting ChimeraX from a terminal.  You might see a
      similar error when installing the next chimerax-daily -- that will
      not have that bug :-).<br class="">
    </p><p class="">    -- Greg<br class="">
    </p>
    <div class="moz-cite-prefix">On 9/9/2022 10:41 AM, Tom Goddard
      wrote:<br class="">
    </div>
    <blockquote type="cite" cite="mid:C426E195-A6A7-4C11-B373-855A222EF0D4@sonic.net" class="">
      <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class="">
      Greg Couch our Linux expert would have to answer that question.
      <div class=""><br class="">
      </div>
      <div class=""><span class="Apple-tab-span" style="white-space:pre">     </span>Tom<br class="">
        <div class=""><br class="">
          <blockquote type="cite" class="">
            <div class="">On Sep 9, 2022, at 1:09 AM, Enrico Martinez
              via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
              wrote:</div>
            <br class="Apple-interchange-newline">
            <div class="">
              <div dir="ltr" class="">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 ?</div>
              <br class="">
              <div class="gmail_quote">
                <div dir="ltr" class="gmail_attr">Il giorno ven 9 set
                  2022 alle ore 10:07 Enrico Martinez <<a href="mailto:jmsstarlight@gmail.com" class="moz-txt-link-freetext" moz-do-not-send="true">jmsstarlight@gmail.com</a>>
                  ha scritto:<br class="">
                </div>
                <blockquote class="gmail_quote" style="margin:0px 0px
                  0px 0.8ex;border-left:1px solid
                  rgb(204,204,204);padding-left:1ex">
                  <div dir="ltr" class="">Thank you Tom!
                    <div class="">Actually I faced the problem with the
                      installation of the chimerax-daily on the
                      ubuntu-20.04 </div>
                    <div class="">(currently I am using the 1.4 version
                      realized in june 2022). Here is the error of the
                      installation:</div>
                    <div class=""><br class="">
                    </div>
                    <div class="">root@Perfetto-7920-Tower:/home/enrico/Downloads#
                      dpkg -i ./chimerax-daily.deb<br class="">
                      (Reading database ... 322925 files and directories
                      currently installed.)<br class="">
                      Preparing to unpack ./chimerax-daily.deb ...<br class="">
                      Deregister desktop menu and associated mime types<br class="">
                      Remove Python cache files<br class="">
                      Unpacking ucsf-chimerax-daily
                      (2022.09.08ubuntu20.04) over
                      (2022.09.08ubuntu20.04) ...<br class="">
                      Setting up ucsf-chimerax-daily
                      (2022.09.08ubuntu20.04) ...<br class="">
                      Install desktop menu and associated mime types<br class="">
                      Traceback (most recent call last):<br class="">
                        File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py",
                      line 724, in init<br class="">
                          run(sess, cmd)<br class="">
                        File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py",
                      line 38, in run<br class="">
                          results = command.run(text, log=log,
                      return_json=return_json)<br class="">
                        File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py",
                      line 2897, in run<br class="">
                          result = ci.function(session, **kw_args)<br class="">
                        File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/cmd.py",
                      line 23, in linux_xdg_install<br class="">
                          install(session, verbose=verbose,
                      system=system)<br class="">
                        File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py",
                      line 428, in install<br class="">
                          generate(session, info, system, verbose)<br class="">
                        File
"/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py",
                      line 421, in generate<br class="">
                          from chimerax.core import localized_app_name<br class="">
                      ImportError: cannot import name
                      'localized_app_name' from 'chimerax.core'
(/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__init__.py)<br class="">
                      dpkg: error processing package ucsf-chimerax-daily
                      (--install):<br class="">
                       installed ucsf-chimerax-daily package
                      post-installation script subprocess returned error
                      exit status 70<br class="">
                      Processing triggers for man-db (2.9.1-1) ...<br class="">
                      Errors were encountered while processing:<br class="">
                       ucsf-chimerax-daily<br class="">
                    </div>
                    <div class=""><br class="">
                    </div>
                  </div>
                  <br class="">
                  <div class="gmail_quote">
                    <div dir="ltr" class="gmail_attr">Il giorno ven 9
                      set 2022 alle ore 00:07 Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">goddard@sonic.net</a>>
                      ha scritto:<br class="">
                    </div>
                    <blockquote class="gmail_quote" style="margin:0px
                      0px 0px 0.8ex;border-left:1px solid
                      rgb(204,204,204);padding-left:1ex">
                      <div class="">Hi Enrico,
                        <div class=""><br class="">
                        </div>
                        <div class="">  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</div>
                        <div class=""><br class="">
                        </div>
                        <div class="">
                          <div class="">from chimerax.core.commands
                            import run</div>
                          <div class="">plot = run(session, 'crosslinks
                            histo #1.1')</div>
                          <div class="">plot.save_plot('histogram.png')</div>
                          <div class=""><br class="">
                          </div>
                          <div class="">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.</div>
                          <div class=""><br class="">
                          </div>
                          <div class="">  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.</div>
                          <div class=""><br class="">
                          </div>
                          <div class=""><span style="white-space:pre-wrap" class="">  </span>Tom</div>
                          <div class=""><br class="">
                          </div>
                          <div class="">Example histogram of hydrogen
                            bond lengths for pdb 7qfc saved with the
                            context menu entry "Save Plot As..."</div>
                          <div class=""><br class="">
                          </div>
                          <div class=""><span id="cid:18321491eb0f0834a9f1" class=""><histogram.png></span></div>
                          <div class=""><br class="">
                            <blockquote type="cite" class="">
                              <div class="">On Sep 8, 2022, at 9:10 AM,
                                Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
                                wrote:</div>
                              <br class="">
                              <div class="">
                                <div class="">Hello,<br class="">
                                  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.
                                    <br class="">
                                  <br class="">
                                  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:<br class="">
                                  <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram</a>><br class="">
                                  <br class="">
                                  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.<br class="">
                                  Best,<br class="">
                                  Elaine<br class="">
                                  -----<br class="">
                                  Elaine C. Meng, Ph.D.
                                                        <br class="">
                                  UCSF Chimera(X) team<br class="">
                                  Department of Pharmaceutical Chemistry<br class="">
                                  University of California, San
                                  Francisco<br class="">
                                  <br class="">
                                  <br class="">
                                  <blockquote type="cite" class="">On
                                    Sep 8, 2022, at 1:40 AM, Enrico
                                    Martinez via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
                                    wrote:<br class="">
                                    <br class="">
                                    Thanks a lot, Elaine!<br class="">
                                    Actually crosslink hist #1 works
                                    very well!<br class="">
                                    Could you please specify would it be
                                    possible to plot the histogram<br class="">
                                    (using batch chimera-x execution) or
                                    alternatively add it directly to<br class="">
                                    the produced png image?<br class="">
                                    I did not find any possibility to
                                    save the plot or to customize its<br class="">
                                    appearance (color of the bars etc).<br class="">
                                    Cheers<br class="">
                                    Enrico<br class="">
                                    <br class="">
                                    Il giorno mer 7 set 2022 alle ore
                                    17:52 Elaine Meng<br class="">
                                    <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">meng@cgl.ucsf.edu</a>>
                                    ha scritto:<br class="">
                                    <blockquote type="cite" class=""><br class="">
                                      Hello!<br class="">
                                      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.<br class="">
                                      <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html</a>><br class="">
                                      <br class="">
                                      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:<br class="">
                                      <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram</a>><br class="">
                                      <br class="">
                                      Also for a more detailed example
                                      see the "Interactive H-bond
                                      Histogram" feature highlight,
                                      which includes a script (.cxc
                                      file):<br class="">
                                      <<a href="https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram</a>><br class="">
                                      <br class="">
                                      I hope this helps,<br class="">
                                      Elaine<br class="">
                                      -----<br class="">
                                      Elaine C. Meng, Ph.D.<br class="">
                                      UCSF Chimera(X) team<br class="">
                                      Department of Pharmaceutical
                                      Chemistry<br class="">
                                      University of California, San
                                      Francisco<br class="">
                                      <br class="">
                                      <br class="">
                                      <blockquote type="cite" class="">On
                                        Sep 7, 2022, at 2:18 AM, Enrico
                                        Martinez via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
                                        wrote:<br class="">
                                        <br class="">
                                        Dear ChimeraX users!<br class="">
                                        I am dealing with the analysis
                                        of protein-ligand interactions
                                        in a<br class="">
                                        single PDB structure. I am
                                        looking for any tools
                                        implemented in<br class="">
                                        Chimera-X, which could be used
                                        to analyse the interactions
                                        (besides<br class="">
                                        the hbond and contact tools
                                        giving info in the log files).<br class="">
                                        I wonder to know which commands
                                        and corresponded ChimeraX tools
                                        could<br class="">
                                        be used to produce the 2D
                                        contact diagrams shown on the
                                        Fig.4 as well<br class="">
                                        as python graphs demonstrated on
                                        the Fig.5 in the Chimera-X
                                        article:<br class="">
                                        <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/</a><br class="">
                                        <br class="">
                                        Many thanks in advance!<br class="">
                                        Cheers<br class="">
                                        Enrico<br class="">
                                      </blockquote>
                                    </blockquote>
                                  </blockquote>
                                  <br class="">
                                  <br class="">
_______________________________________________<br class="">
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                                  Manage subscription:<br class="">
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                              </div>
                            </blockquote>
                          </div>
                          <br class="">
                        </div>
                      </div>
                    </blockquote>
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              </div>
              _______________________________________________<br class="">
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      </div>
    </blockquote>
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