[Chimera-users] Displaying Surface For Selected Residues

[Eric Pettersen]

On Oct 7, 2009, at 4:33 PM, Thiruvarangan Ramaraj wrote:

> Thanks Eric, but just to follow up on the surf sel command,
>
> It displays the surface for the selected residues,
>
> does it assign solvent-excluded and solvent-accessible surface areas  
> per atom and residue to attributes named  areaSES and areaSAS to the  
> selected residues or to the whole protein?.
>
> after I do  "surf sel" I have select:/areaSAS > 50 , looks like it  
> selects for the whole protein. Shouldn't it show only for the  
> selected surface region.
>

Hi Thiru,
	Surfaces are computed for the entirety of the molecule (that the  
surface covers), not just the residues you display the surface on.  So  
therefore other residues also got areaSAS/SES attributes.  To get what  
you want I think you need:

	sel :/areaSAS > 50 & @/surfaceDisplay

--Eric
	
> Thanks
>
> -Thiru
>
> --- On Wed, 10/7/09, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: Displaying Surface For Selected Residues
> To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
> Date: Wednesday, October 7, 2009, 5:14 PM
>
> Yes, most commands work on everything if you don't specify what to  
> work on.  For instance "color red" colors everything red whereas  
> "color red sel" colors the selection red.
>
> --Eric
>
> On Oct 7, 2009, at 4:09 PM, Thiruvarangan Ramaraj wrote:
>
>> Worked fine, Thanks, Eric
>>
>> -Thiru
>>
>> --- On Wed, 10/7/09, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>
>> From: Eric Pettersen <pett at cgl.ucsf.edu>
>> Subject: Re: Displaying Surface For Selected Residues
>> To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
>> Date: Wednesday, October 7, 2009, 5:04 PM
>>
>> "surface sel"
>>
>> --Eric
>>
>> On Oct 7, 2009, at 4:03 PM, Thiruvarangan Ramaraj wrote:
>>
>>> Hi Eric,
>>>
>>> I have a protein with a few residues selected, and I wanted to  
>>> show surface only on the selected residues, when I go to Actions -  
>>> Surface -Show , it shows surface only for the selected residues,  
>>> but when I use the command surface on the command line it shows  
>>> the surface for the entire protein.  Is there a command line  
>>> option to show surface only for the selected residues on the  
>>> protein.
>>>
>>> Thanks
>>>
>>> Thiru
>>>
>>> --- On Thu, 10/1/09, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>>
>>> From: Eric Pettersen <pett at cgl.ucsf.edu>
>>> Subject: Re: [Chimera-users] Solvent Accessible Surface Area
>>> To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
>>> Cc: "UCSF Chimera Mailing List" <chimera-users at cgl.ucsf.edu>
>>> Date: Thursday, October 1, 2009, 3:38 PM
>>>
>>> Oops, spotted a bug in the script.  This line:
>>>
>>> out = open(os.path.expanduser("~/out", "w"))
>>>
>>> should be:
>>>
>>> out = open(os.path.expanduser("~/out"), "w")
>>>
>>> --Eric
>>>
>>>
>>>
>>
>>
>
>

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