My feeling is that a request to the APBS users list would be the most likely way to get a plugin sooner rather than much, much later. ;-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 9, 2012, at 11:54 AM, sette@uniroma2.it wrote:
Hi,
in which way we could help? Multiple requests to the APBS mailing list is sufficient ?
Marco
Tom Goddard <goddard@sonic.net> ha scritto:
Some of the difficulties in putting APBS into Chimera are: 1) There are a lot of parameters in an APBS calculation, 2) It can take a lot of memory when running (I recall 1 Gbyte for a few thousand atom protein), 3) It can take a long time to compute.
None of these prevent it from going in to Chimera but to make it work well requires significant work. Someone would have to decide which are the most important parameters to allow the user to change. It might be very helpful to estimate the peak memory usage for instance when choosing grid spacing since once it exceeds the physical memory of the machine it will be extremely slow and could make the machine unusable while it runs. It also should not freeze Chimera when running since even a modest computation takes minutes I think.
Tom
Yeah, there were some tentative feelers about such a plugin a couple of years back, but it fizzled out. If you made a request on the APBS-users list (SourceForge.net: Mailing Lists for APBS <http://sourceforge.net/mail/?group_id=148472
) they might consider it.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jan 6, 2012, at 7:25 AM, Boaz Shaanan wrote:
Hi Elaine,
Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too?
Happy New Year to you all (still not too late).
Boaz
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328
www.rete29aprile.it
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