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) 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