[Chimera-users] Local execution of pdb2pqr and APBS

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Dec 16 09:55:05 PST 2013


Hi Conrad,

I think it will be OK in my scripts for now, but eventually I will need this functionality for a web server we're developing. I think it unlikely that we'll get permission from our security folks to have our web server send jobs to an external web server and retrieve those results. This is why I need to do it locally.

I'll download the daily build and give this a try. I'll let you know ASAP.

Thanks!
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

From: Conrad Huang <conrad at cgl.ucsf.edu<mailto:conrad at cgl.ucsf.edu>>
Date: Monday, December 16, 2013 12:51 PM
To: Darrell Hurt <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>>, "'chimera-users at cgl.ucsf.edu<mailto:'chimera-users at cgl.ucsf.edu>'" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Local execution of pdb2pqr and APBS

Ah.  Well.  Ermmm.

It's not possible right now due to an oversight on my part.  Although
the functionality was all implemented, there is no way to invoke it.
I've added some code to the command lines for apbs, pdb2pqr and vina.
There are now three additional optional arguments to those commands:

- backend = "opal" | "local"
- service = Opal service name | path to executable
- url = Opal URL | unused

So a command like:

apbs backend local service /tmp/myapbs

should initiate a local computation process.  I say "should" because
I've not installed APBS on my machine and am a little too busy to do it
today.  However, when I test the above command, it does tell me that
/tmp/myapbs is not an executable file, so the code at least somewhat
works.  I thought I'd make that available in the daily build for
tomorrow and let someone "volunteer" to test it. :-)   If you do have a
chance to test it, please let me know whether it works.  I'll install
and test it with apbs on my machine in the next couple days in any case.

Conrad

On 12/16/2013 6:05 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi Chimera friends,

Sorry to bother you again with so many questions.

I'm trying to use PDB2PQR and APBS in a script to calculate an EP
map. I know how to specify a local executable location for these
external applications if I use the graphics interface, but the
documentation that I can find does not indicate how to do this via
the command line. Is it possible? How do I do it?

Thanks! Darrell

-- Darrell Hurt, Ph.D. Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office:
301-402-0095 Mobile: 301-758-3559 Web: BCBB Home
Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>


Twitter: @niaidbioit<https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments
is confidential and may contain sensitive information. It should not
be used by anyone who is not the original intended recipient. If you
have received this e-mail in error please inform the sender and
delete it from your mailbox or any other storage devices. National
Institute of Allergy and Infectious Diseases shall not accept
liability for any statements made that are sender's own and not
expressly made on behalf of the NIAID by one of its representatives.

_______________________________________________ Chimera-users mailing
list Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users






More information about the Chimera-users mailing list