Re: [Chimera-users] APBS interface in Chimera
Hi Boaz, It is brand new, so you have not at all been negligent! I only documented it a few days ago. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> Currently it does not have the option to use a locally installed APBS -- it uses an APBS web service provided by the National Biomedical Computation Resource. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 8, 2012, at 9:24 AM, Boaz Shaanan wrote:
Hi, Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams!
Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something?
Cheers, Boaz
Hi Elaine, Thanks a lot. I'll give a try soon. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Monday, October 08, 2012 6:34 PM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu; Baker, Nathan Subject: Re: [Chimera-users] APBS interface in Chimera Hi Boaz, It is brand new, so you have not at all been negligent! I only documented it a few days ago. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> Currently it does not have the option to use a locally installed APBS -- it uses an APBS web service provided by the National Biomedical Computation Resource. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 8, 2012, at 9:24 AM, Boaz Shaanan wrote:
Hi, Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams!
Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something?
Cheers, Boaz
Hi Elaine -- This is great news! Would you be interested in talking more about this extension at some point to discuss ways to make the Chimera/APBS user interface as user-friendly as possible? Thanks, -- Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me On 10/8/12 11:34 AM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Boaz, It is brand new, so you have not at all been negligent! I only documented it a few days ago. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
Currently it does not have the option to use a locally installed APBS -- it uses an APBS web service provided by the National Biomedical Computation Resource. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2012, at 9:24 AM, Boaz Shaanan wrote:
Hi, Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams!
Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something?
Cheers, Boaz
The current user interface is designed as a front-end to the APBS web service hosted by the National Biomedical Computation Resource (NBCR) and thus offers (some of) the functionality provided by the web interface. We would certainly be interested in how the tool might be used in real situations and what we can do to facilitate that. Conrad On 10/8/12 7:36 PM, Baker, Nathan wrote:
Hi Elaine --
This is great news! Would you be interested in talking more about this extension at some point to discuss ways to make the Chimera/APBS user interface as user-friendly as possible?
Thanks,
participants (4)
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Baker, Nathan -
Boaz Shaanan -
Conrad Huang -
Elaine Meng