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<p class="MsoNormal">Hi Eric,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Good day!!<o:p></o:p></p>
<p class="MsoNormal">Thanks much for sharing the details.<o:p></o:p></p>
<p class="MsoNormal">If we need more information we shall connect you.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks you in advance for your help and support.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards,<o:p></o:p></p>
<p class="MsoNormal">Siddhartha<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu> <br>
<b>Sent:</b> Monday, April 12, 2021 11:31 PM<br>
<b>To:</b> Siddhartha Pradhan (Contractor) <siddhartha.pradhan1@gilead.com><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Siddhartha,<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>When Chimera starts up, it may contact
<a href="https://urldefense.com/v3/__http:/www.cgl.ucsf.edu__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaN_idOu24$">
www.cgl.ucsf.edu</a> to determine if a newer version of Chimera is available and alert the user if there is one. The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites→Preferences).<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness. It would not be able to fetch data from publicly
available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things.<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results. They are:
comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE. It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service. As
far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures. There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory).<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">--Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Eric Pettersen<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>UCSF Computer Graphics Lab<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
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<o:p></o:p></p>
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<p class="MsoNormal">On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <<a href="mailto:siddhartha.pradhan1@gilead.com">siddhartha.pradhan1@gilead.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<li class="MsoListParagraph" style="margin-top:0in;margin-bottom:0in;margin-bottom:.0001pt;mso-list:l0 level1 lfo1">
Connection to <a href="https://urldefense.com/v3/__http:/169.230.27.29__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNSBeZYQY$">
169.230.27.29</a> on tcp/80 (<a href="https://urldefense.com/v3/__http:/www.cgl.ucsf.edu/__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNhFT045w$"><span style="color:#954F72">www.cgl.ucsf.edu</span></a>)<o:p></o:p></li></ol>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">• Why the network connection is being made and what is the reason behind it?<o:p></o:p></p>
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<p class="MsoNormal">• Is there any sorts of data transfer is being happened from the user system?<o:p></o:p></p>
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<p class="MsoNormal">• Is there any settings in the application to disable the network connections?<o:p></o:p></p>
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<p class="MsoNormal">• If users can use the software to export/import data. Is there any cloud service associated with this?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">It would be of great help if you can kindly give a clarity for the above network connection ASAP.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Regards,<o:p></o:p></p>
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<p class="MsoNormal">Siddhartha<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
Chimera-users mailing list:<span class="apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">Chimera-users@cgl.ucsf.edu</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
Manage subscription:<span class="apple-converted-space"> </span></span><a href="https://urldefense.com/v3/__https:/plato.cgl.ucsf.edu/mailman/listinfo/chimera-users__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNxBkYCHg$"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</span></a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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