[Chimera-users] Troubleshooting request for help

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 28 08:26:15 PDT 2020

It would have helped if the question had actually stated the problem!  If they are .py and .pyc files they might be "Chimera session files" which somebody could have created with Chimera, but they could also be some other python files that are not Chimera sessions.

(1) I do not see a problem in this screenshot, only a bunch of files and some information dialogs.  Is there an error message of some kind if you try to open any of them with Chimera?

(2) As far as I know, files with these names are not included in any downloaded software and do not appear anywhere on our website. How did you find any of these files, and what information are you expecting them to contain?  Since I don't believe we provide any of those files, Tanuja would have to ask the third party (whoever made them) if they are Chimera sessions.  If they are Chimera sessions, she might need to use a different version of Chimera, i.e. at least as new as the version that was used to make them.

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

> On Sep 28, 2020, at 6:54 AM, Goins, Jerquan (NIH/NCI) [C] <jerquan.goins at nih.gov> wrote:
> Hi, 
> I've attached a screen shot of the problem she's having. She's unable to open that mutation file. She mentioned she got it from your website. I tried to find it so that she can maybe download it in the proper format. She explained that it was a file that came with the installation. Is there any way you guys can be of assistance I'd highly appreciate it. 
> Jerquan Goins (Contractor)
> Desktop Support Technician
> Team GRSi
> National Cancer Institute
> Center for Biomedical Informatics and Information Technology
> Building 10, 10 Center Drive Bethesda Maryland, 20892
> Email: Jerquan.Goins at nih.gov
> Phone: 2407606706
> On 9/25/20, 6:47 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>    Hi Tanuja,
>    The address for asking Chimera questions is chimera-users at cgl.ucsf.edu, CC'd here.
>    Probably you were using some tools that call web services: PDB2PQR, APBS, and/or Autodock Vina.  These web services were provided by another group (not our lab) and they have been discontinued, sorry.
>    There are suggestions of what you could do instead in the help pages for these tools in Chimera:
>    <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
>    <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
>    <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>    Probably for APBS and PDB2PQR the simplest approach is to skip Chimera and use the web service at 
>    <http://server.poissonboltzmann.org/>
>    If you were trying to do docking, besides the Vina  help link above, there are several posts to the chimera-users list with suggestions of alternatives, for example:
>    <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017079.html>
>    <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017126.html>
>    I hope this helps,
>    Elaine
>    -----
>    Elaine C. Meng, Ph.D.                       
>    UCSF Chimera(X) team
>    Department of Pharmaceutical Chemistry
>    University of California, San Francisco
>> On Sep 25, 2020, at 2:13 PM, Cain, Cheryl A <Cheryl.Cain at ucsf.edu> wrote:
>> Hi Tanuja, 
>> I've added chimera-users at cgl.ucsf.edu to this email as they should be able to help you there.
>> Thanks,
>> Cheryl
>> Cheryl Cain
>> cheryl.cain at ucsf.edu
>> Operations Coordinator, Department of Pharmaceutical Chemistry
>> Accreditation Project Coordinator, School of Pharmacy
>> From: Saswat, Tanuja (NIH/NCI) [F] <tanuja.saswat at nih.gov>
>> Sent: Friday, September 25, 2020 9:56 AM
>> To: chimera at cgl.ucsf.edu <chimera at cgl.ucsf.edu>
>> Cc: Goins, Jerquan (NIH/NCI) [C] <jerquan.goins at nih.gov>
>> Subject: Troubleshooting request for help
>> Hi, 
>> I am a researcher at the NIH who uses this software to complete analysis. But as of recently some of the features that I usually use have not been able to access them. Can you guys assist me in finding a resolution. 
>> I’ve CC’s my IT support in case there was something above my cresds level.
>> Regards
>> --
>> Tanuja Saswat, Ph.D.
>> Postdoctoral Research Fellow
>> Laboratory of Dr. Laurie T. Krug
>> HIV and AIDS Malignancy Branch (HAMB)
>> Center for Cancer Research
>> National Cancer Institute
>> tanuja.saswat at nih.gov
>> Building 10, Room 4A08
>> Ph:240-858-3201
>> NCI Website
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> <Screen Shot 2020-09-25 at 1.26.38 PM.png>

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