[Chimera-users] {Disarmed} Re: APBS -> Chimera plugin - why not?

sette at uniroma2.it sette at uniroma2.it
Mon Jan 9 11:54:38 PST 2012


in which way we could help?
Multiple requests to the APBS mailing list is sufficient ?


Tom Goddard <goddard at 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 at uniroma2.it
e-mail:        m77it at yahoo.it
Tel.:          +39-0672594424
Fax:           +39-0672594328


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