Balazs is right. If you only select the nucleic acid, it will calculate the
SASA of just the selection as though everything else that HASN'T been
selected isn't even there. Then you can imagine that the binding forces the
NA into a rather distorted conformation which has a higher surface area than
the non-distorted version.
Balazs' instructions appear correct, I was just giving the explanation as to
why your surface area appeared larger.
Good luck!
Jason
On Wed, May 5, 2010 at 7:53 AM, Balazs Jojart <jojartb.gmail.com> wrote:
> Hi Geyan,
> I made a mistake in the selection:
> instead of and you have to use *OR*
> set all [atomselect top "protein or nucleic"]
> HTH
> Balazs
>
>
>
> Balazs Jojart wrote:
>
>> Hi Geyan,
>> I think you can use the following commands:
>> set all [atomselect top "protein and nucleic"]
>> set prot [atomselect top "protein"]
>> set nucleic [atomselect top "nucleic"]
>> measure sasa 1.4 $all -restrict $prot
>> measure sasa 1.4 $all -restrict $nucleic
>> the first measure will contain only the contribution of the protein, and
>> the second one the contribution of the nucleic acid to the whole surface.
>> HTH,
>> Balazs
>>
>>
>> geyan wrote:
>>
>>> Hello Balazs,
>>> With your previous reply about the molecular surface area calculation,I
>>> write this email to you and hope you can help me.
>>> Now I meet a abnormal phenomenon.I have a system of DNA-Protein
>>> complex.This kind of protein can compass the DNA to protect it from
>>> damage.So it's reasonable that the surface area of the DNA is decreasing
>>> with the binding of the protein.But with the command in VMD,that is "set dna
>>> [atomselect top "dna"] " and "measure sasa 1.4 $dna",the result is opposite
>>> to arrise.So can you tell me why the value of the surface area is becoming
>>> larger after binding?What I meant to do is to quantify the protection of the
>>> protein to DNA by calculating the exact reduction of the surface area of
>>> the DNA.
>>> Thanks advance.
>>>
>>>
>>> 2010-05-05
>>>
>>>
>>> geyan
>>>
>>>
>>> 发件人： Balazs Jojart 发送时间： 2010-04-23 14:28:00 收件人： AMBER Mailing List 抄送：
>>> 主题： Re: [AMBER] molecular surface area Hello Geyan,
>>> see my previous post about this issue:
>>> http://archive.ambermd.org/201003/0585.html
>>> HTH
>>> Balazs
>>> geyan wrote:
>>>
>>>
>>>> Has anybody done this analysis before?
>>>> I want to focus on the protection of protein to DNA.Now there is a
>>>> interesting thing,when the DNA is in nature,the surface area is one
>>>> figure,when the protein bind to it, both the surface area of protein and DNA
>>>> will change,from which we can measure the protection effect.
>>>> My question is how to quantify the surface area.which program can do
>>>> this well and easily?I think amber is powerful enough to figure it out
>>>> easily,but how?
>>>> Many thanks.
>>>> --------------
>>>> geyan
>>>> 2010-04-23
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 05 2010 - 07:00:06 PDT
