<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class="">
<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="">
ChimeraX-users mailing list<br class="">
<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><br class="">
Manage subscription:<br class="">
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank" class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class="">
<br class="">
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
_______________________________________________<br class="">
ChimeraX-users mailing list<br class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="moz-txt-link-freetext" moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br class="">
Manage subscription:<br class="">
<a class="moz-txt-link-freetext" href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</blockquote>
</div>
</body></html>