[Chimera-users] APBS -> Chimera plugin - why not?

Tom Goddard goddard at sonic.net
Mon Jan 9 11:15:34 PST 2012

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.


> 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

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