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
>>>
>>>
>>>
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>>>
>>>
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Received on Wed May 05 2010 - 05:00:03 PDT
