Changes between Version 3 and Version 4 of PrivacyAndSecurity

Timestamp:

Dec 4, 2025, 4:46:20 PM (8 hours ago)

Author:

Tom Ferrin

Comment:

A little wordsmithing and typo corrections.

PrivacyAndSecurity

@@ -5 +5 @@
 ChimeraX makes use of web services to retrieve data from databases and perform advanced calculations.  This page describes services that may send data from your computer to outside services.
 
-In general the files you create and view on your computer are not sent over the network unless you explicitly use ChimeraX tools documented to use web services. You don't need to be on the internet to use the program, but it is definitely more convenient to have internet connectivity, for fetching data from databases (protein data bank, EM data bank, !UniProt, etc.) and using tools that rely on web services (multiple sequence alignment, Modeller comparative modeling, etc.).  
+In general the files you create and view on your computer are not sent over the network unless you explicitly use ChimeraX tools documented to use web services. You don't need to be on the internet to use the program, but it is definitely more convenient to have internet connectivity for fetching data from databases (protein data bank, EM data bank, !UniProt, etc.) and using tools that rely on web services (multiple sequence alignment, Modeller comparative modeling, etc.).  
 
 == Databases ==
 
-Fetching atomic models or experimental data from databases such as the PDB, EMDB, !AlphaFold database, !PubChem, !UniProt, and many others sends the ID codes or search test you specify to those database sites.  The ChimeraX documentation lists the databases used to fetch data via ChimeraX commands
+Fetching atomic models or experimental data from databases such as the PDB, EMDB, !AlphaFold database, !PubChem, !UniProt, and many others sends the ID codes or the search text you specify to those database sites.  The ChimeraX documentation lists the databases used to fetch data via ChimeraX commands
 [https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch Online sources] and the [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html Fetch By Id] graphics user interface.
 
@@ -16 +16 @@
 Some of the ChimeraX analysis tools use web services and this is clearly documented in their individual help pages.
 
-The ChimeraX documentation provides a [https://rbvi.ucsf.edu/chimerax/docs/webservices.html list of web services] potentially used by ChimeraX, depending on what tools/features are invoked by the user.
+The ChimeraX documentation provides a [https://rbvi.ucsf.edu/chimerax/docs/webservices.html list of web services] used by ChimeraX, depending on what specific tools/features are invoked by the user.
 
-If the user runs ChimeraX tools that depend on web services, that will send data needed for that calculation over the network, e.g. the sequences will be sent to the web server running the multiple sequence alignment program.
+If a user runs a ChimeraX tool that depends on web services, data needed for that calculation will be sent over the internet, e.g. the sequences will be sent to the web server running the multiple sequence alignment program.
 
-Here are a few examples. The !AlphaFold structure prediction serve will send data to Google Colab, and using it requires that user to sign in to Google first.  The Boltz prediction service runs the calculation on the local computer but sends protein sequences to the Colabfold sequence alignment server.  The Modeller structure homology service sends sequences and provided structure templates to the UCSF Modeller service.
+Here are a few examples: The !AlphaFold structure prediction service will send data to Google Colab, and using it requires that the user to sign in to Google first.  The Boltz prediction service runs the structure prediction calculation on the user's local computer, but sends protein sequences to the Colabfold sequence alignment server as part of the process.  The Modeller structure homology service sends sequences and provided structure templates to the UCSF Modeller service.
 
-== Check for updates ==
+== Check for Updates ==
 
-ChimeraX periodically checks for newer versions of the program and third-party plugins.  This check is done by default weekly, however, if the network is not available, it will not do the checks.  There is an [https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#toolshed option in the user preferences dialog] to change the frequency of checking including the option to "never check".
+ChimeraX periodically checks for newer versions of the program and third-party plugins and notifies the user if a newer version is available.  This check is done by default weekly, however, if the network is not available, it will not perform the checks.  There is an [https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#toolshed option in the user preferences dialog] to change the frequency of checking, including the option to "never check."
 
-== Bond connectivity templates ==
+== Bond Connectivity Templates ==
 
 When you open atomic structure mmCIF files ChimeraX will determine bond connectivity of non-standard residues and ligands by looking up templates at the Protein Databank if those templates have not already been cached on your computer.  If the network is not available, the connectivity will be guessed.
@@ -32 +32 @@
 == Registration ==
 
-When you download the program, we record the IP address of the download.  After 15 separate days of use ChimeraX will ask you to register.  [https://www.cgl.ucsf.edu/chimerax/docs/user/tools/registration.html Registration] is voluntary and requires internet connectivity.  Any information you provide on the [https://www.rbvi.ucsf.edu/chimerax/cgi-bin/chimerax_registration.py registration form] (name, email, interests) are sent to the ChimeraX lab and will not be shared.  It is not required to register but the registration panel will appear at the start of each session after 15 days of use if you have not registered.
+When you download the program, we record the IP address of the download.  After 15 separate days of use ChimeraX will ask you to register.  [https://www.cgl.ucsf.edu/chimerax/docs/user/tools/registration.html Registration] is voluntary and requires internet connectivity.  Any information you provide on the [https://www.rbvi.ucsf.edu/chimerax/cgi-bin/chimerax_registration.py registration form] (name, email, research interests) are sent to our UCSF ChimeraX research lab but are not shared.  It is not required to register but the registration panel will then appear at the start of each session after 15 days of use if you have not registered.
 
-== Bug reporting ==
+== Bug Reporting ==
 
-If an error occurs in ChimeraX you may see a panel with a button to "Report a Bug".  Bug reports go into a publicly visible database.  They include the Log which shows the commands and user interface tools you used and names of files you opened unless you uncheck the button "Include log contents in bug reports".  You may attach files to the bug report and those will also be public.  You should not provide any confidential or private data in bug reports.
+If an error occurs in ChimeraX you may see a panel with a button to "Report a Bug."  Bug reports go into a publicly visible database.  They include the session Log which shows the ChimeraX commands that caused the error and user interface tools you used and names of files you opened unless you uncheck the button "Include log contents in bug reports." You optionally may attach data files to the bug report and those will also be publicly visible. ''You should not provide any confidential or private data in bug reports.''
 
 == Remote Control of ChimeraX ==
@@ -42 +42 @@
 A few capabilities of ChimeraX allow other programs to connect to and control ChimeraX.  None are enabled by default.  These are the [https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/restserver/restserver.html REST Server] and [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/meeting.html Meeting Tool].
 
-== ChimeraX code ==
+== ChimeraX Third-Party Software Libraries ==
 
-The ChimeraX software relies on over 100 third-party open-source packages.  The code developed by the UCSF RBVI lab is all [https://github.com/RBVI/ChimeraX/ available at Github].  The [https://github.com/RBVI/ChimeraX/blob/develop/pyproject.toml pyproject.toml] source file lists the packages from the Python !PyPi package management system that are included. A more extensive list of [https://www.rbvi.ucsf.edu/chimerax/docs/embedded.html software embedded in ChimeraX] including packages in other languages (e.g. !AmberTools, ffmpeg, ...) is provided in the documentation.
+ChimeraX relies on over 100 third-party open-source software packages.  The code developed by our UCSF our research lab is [https://github.com/RBVI/ChimeraX/ available at Github].  The [https://github.com/RBVI/ChimeraX/blob/develop/pyproject.toml pyproject.toml] source file lists the packages from the Python !PyPi package management system that are included. A more extensive list of [https://www.rbvi.ucsf.edu/chimerax/docs/embedded.html software embedded in ChimeraX] including packages in other languages (e.g. !AmberTools, ffmpeg, ...) is provided in the documentation.
 
 == ChimeraX Toolshed ==
 
-Plugins to ChimeraX can be downloaded from the [https://cxtoolshed.rbvi.ucsf.edu Toolshed web site] using ChimeraX menu entry Tools / More Tools....  These plugins are developed by third-party developers not affiliated with the UCSF ChimeraX lab.  While we test the plugins when the are first put on the Toolshed app store any privacy and security issues are the responsibilities of the plugin developers.
+Plugins to ChimeraX can be downloaded from the [https://cxtoolshed.rbvi.ucsf.edu Toolshed web site] using the ChimeraX menu entry Tools / More Tools....  These plugins are developed by third-party developers not affiliated with our UCSF ChimeraX lab.  While we test the plugins when they are first put on the Toolshed app store, any privacy and security issues are the responsibilities of the plugin developers.