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

[Eric Pettersen]

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 at uniroma2.it wrote:

>
> Hi,
>
> in which way we could help?
> Multiple requests to the APBS mailing list is sufficient ?
>
> Marco
>
>
>
> 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
>
> www.rete29aprile.it
>
>
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