[Chimera-users] Using APBS via UCSF-Chimera
Elaine Meng
meng at cgl.ucsf.edu
Fri Apr 24 09:43:08 PDT 2020
Hi Boaz,
It is not simply changing the URL (which you can actually do yourself in the "Executable location" options of APBS and PDB2PQR) because even if the web services are running there, as far as I can tell their access mechanism has changed. The Chimera tools are written to work with OPAL services and I'm guessing these are or will be REST interfaces, since the URL has "rest" in it. Given limited resources/manpower, I can't say anything other than no at this time.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Apr 24, 2020, at 9:06 AM, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:
>
> Hi Elaine,
>
> There has been a recent message on the pdb2pqr/apbs bb about transferring the programs to a new site:
> http://apbs-rest-test.westus2.cloudapp.azure.com/
>
> Would it be possible to access APBS via Chimera in the new location?
>
> Below please find pasted the message from Nathan Baker about the site change:
>
> ------------------------
> Hello –
>
> I’m sorry about the problems you are experiencing. Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem?
>
> Thank you,
>
>
> --
> Nathan Baker
> Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
> Department of Applied Mathematics — University of Washington
> +1-509-375-3997 — https://www.linkedin.com/in/nathanandrewbaker/
>
> ---------------------------------
>
> Stay safe!
>
> Boaz
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: bshaanan at bgu.ac.il
> Phone: 972-8-647-2220
> Fax: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
> ________________________________________
> From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of chimera-users-request at cgl.ucsf.edu <chimera-users-request at cgl.ucsf.edu>
> Sent: Friday, April 24, 2020 6:03 AM
> To: chimera-users at cgl.ucsf.edu
> Subject: Chimera-users Digest, Vol 204, Issue 25
>
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> Today's Topics:
>
> 1. Autodock Vina, APBS, PDB2PQR web services will be removed
> (Elaine Meng)
> 2. Re: Autodock Vina, APBS, PDB2PQR web services will be removed
> (Gregory Babbitt)
> 3. Re: Autodock Vina, APBS, PDB2PQR web services will be removed
> (Elaine Meng)
> 4. Re: Imagine processing from gromacs (benjamintam)
> 5. Session opening issue (Zheng, Fengwei)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 23 Apr 2020 15:20:14 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: "chimera-users at cgl.ucsf.edu List" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services
> will be removed
> Message-ID: <D0F537B2-0035-4D11-99A5-37D783428E2B at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Chimera users,
>
> The Autodock Vina, APBS, and PDB2PQR tools in Chimera rely on web services provided by another lab, the National Biomedical Computation Resource. However, these web services are scheduled to be retired on April 30, 2020.
>
> When that happens, the Autodock Vina, APBS, and PDB2PQR tools in Chimera will no longer work, except for the (very few) people who use the tools to run locally installed copies of the program instead of the web services.
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 23 Apr 2020 22:30:14 +0000
> From: Gregory Babbitt <gabsbi at rit.edu>
> To: "chimera-users at cgl.ucsf.edu List" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services
> will be removed
> Message-ID: <1587681014069.66026 at rit.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks Elaine
>
> I am also curious about the future of the Modeller tool to refine loops via homology.
>
> will that also phase out?
>
> Dr. Gregory A Babbitt
> Associate Professor
> T.H. Gosnell School of Life Sciences
> Rochester Institute of Technology
> Rochester NY USA
> software website: http://people.rit.edu/gabsbi
> YouTube channel https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw
>
>
> ________________________________________
> From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Thursday, April 23, 2020 6:20 PM
> To: chimera-users at cgl.ucsf.edu List
> Subject: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed
>
> Dear Chimera users,
>
> The Autodock Vina, APBS, and PDB2PQR tools in Chimera rely on web services provided by another lab, the National Biomedical Computation Resource. However, these web services are scheduled to be retired on April 30, 2020.
>
> When that happens, the Autodock Vina, APBS, and PDB2PQR tools in Chimera will no longer work, except for the (very few) people who use the tools to run locally installed copies of the program instead of the web services.
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 23 Apr 2020 15:39:07 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Gregory Babbitt <gabsbi at rit.edu>
> Cc: "chimera-users at cgl.ucsf.edu List" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services
> will be removed
> Message-ID: <3E51C8AE-0F6C-4333-B665-D361CF8AC05D at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Gregory,
> The other web services used by Chimera (Modeller, Blast Protein, Clustal Omega, MUSCLE, and others) won't be affected at this time because they're provided by our lab (RBVI), not the NBCR.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>> On Apr 23, 2020, at 3:30 PM, Gregory Babbitt <gabsbi at rit.edu> wrote:
>>
>> Thanks Elaine
>>
>> I am also curious about the future of the Modeller tool to refine loops via homology.
>>
>> will that also phase out?
>>
>> Dr. Gregory A Babbitt
>> Associate Professor
>> T.H. Gosnell School of Life Sciences
>> Rochester Institute of Technology
>> Rochester NY USA
>> software website: http://people.rit.edu/gabsbi
>> YouTube channel https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 24 Apr 2020 02:36:10 +0000
> From: benjamintam <benjamintam at um.edu.mo>
> To: chimera-users <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Imagine processing from gromacs
> Message-ID: <a758179c585148ca91c07ceefbbc1134 at UMMBX3.pclan.umac.mo>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Eric,
>
> Thank you very much for your help. Although I am not sure whether is the university or the mailing list blocked the code content. Nevertheless, I appreciate your help.
>
> Best regards,
>
> Ben
>
> Ph.D, M.Eng, FHEA
>
> From: Eric Pettersen<mailto:pett at cgl.ucsf.edu>
> Sent: 24 April 2020 02:51
> To: benjamintam<mailto:benjamintam at um.edu.mo>
> Cc: chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Imagine processing from gromacs
>
> Hi Ben,
> Typically, one "wraps" a PBC trajectory to produce a new trajectory where molecules stay whole on one side of the box or the other. For Gromacs, the tool for that is trjconv, perhaps with the "-pbc whole" flags. See this page: gmx trjconv - GROMACS 2018 documentation<https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2furldefense.proofpoint.com%2fv2%2furl%3fu%3dhttp%2d3A%5f%5fmanual.gromacs.org%5fdocumentation%5f2018%5fonlinehelp%5fgmx%2d2Dtrjconv.html%26d%3dDwMFaQ%26c%3dKXXihdR8fRNGFkKiMQzstu%2d8MbOxd1NuZkcSBymGmgo%26r%3dEElAJhvpEXZIOG4aO3Q%5f1Fg1wh%2diIcDTLJ2t8QVMlxU%26m%3dpJfYo02dBWyMImWhNt9SQhEshAF42kEnCABBWjH3NjM%26s%3dVfw1MLZfC1pHcWEsIFazzl3tZ%2d0l%2dfHmOMBi6IeaOBs%26e%3d&umid=1193A768-A400-A205-949C-BD11EB526413&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-17b8b3991cfc711054f4afcfdd51feb0f255c2ed>.
> If wrapping a trajectory is problematic for some reason, you could define a per-frame Python script to hide long bonds. I have attached such a script. To use it, in the MD Movie GUI choose the Per-Frame?Define script... menu entry, and in the resulting dialog change the script type to "Python" and use the "Insert text file" button near the button to insert the attached Python file. Then click OK. Long bonds should disappear and you can play your trajectory and bonds will be hidden and shown appropriately.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
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> ------------------------------
>
> Message: 5
> Date: Fri, 24 Apr 2020 02:59:44 +0000
> From: "Zheng, Fengwei" <Fengwei.Zheng at vai.org>
> To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] Session opening issue
> Message-ID:
> <DM6PR01MB610662D9361D8334C56E39D5F1D00 at DM6PR01MB6106.prod.exchangelabs.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear developer,
>
> There is an issue show up when I open a chimeraX session made from another computer(windows 10, chimeraX version 0.93) in macOS(chimeraX version 0.92). Here is the picture, could you tell me the possible reason? I can't fix it at present. Thank you very much!
> [cid:7792cf91-9e23-4a3a-8fc1-1b8e33f932a9]
>
> Be safe,
> Fengwei
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