[Chimera-users] Troubleshooting request for help

[Goins, Jerquan (NIH/NCI) [C]]

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
    > UCSF
    > 
    > 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


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