[Chimera-users] [EXTERNAL] Re: Need help- Why there is network connection

Siddhartha Pradhan (Contractor) siddhartha.pradhan1 at gilead.com
Mon Apr 12 23:44:19 PDT 2021

Hi Elaine,

Good day!!
Thanks much for sharing the details.
If we need more information, we shall connect you.

Thanks much for your help and support in advance.


-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Monday, April 12, 2021 11:46 PM
To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection

Hi Siddhartha,
This page lists the web services (and databases on the web) that may be accessed by Chimera, depending on which features you use and which data you fetch:

<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/webservices.html__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloKAxwyMw$ >

Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 12, 2021, at 11:00 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hi Siddhartha,
> 	When Chimera starts up, it may contact https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloM5McTW0$  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).
> 	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.
> 	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).
> --Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>> On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1 at gilead.com> wrote:
>> Hi, 
>> 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.
>> 	• Connection to https://urldefense.com/v3/__http://;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloHTjBBII$  on tcp/80 (https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_dsWHbFDaUmYPMynZlXX2hiU9eIZtSqgcYBShnTSiNkMlknIubieloM5McTW0$ )
>> •             Why the network connection is being made and what is the reason behind it?
>> •             Is there any sorts of data transfer is being happened from the user system?
>> •             Is there any settings in the application to disable the network connections?
>> •             If users can use the software to export/import data. Is there any cloud service associated with this?
>> It would be of great help if you can kindly give a clarity for the above network connection ASAP.
>> Regards,
>> Siddhartha

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