VMD-L Mailing List

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Mon Feb 07 2005 - 12:03:46 CST

Hi John,
   I'm confused about what the "selection" is in the restrict option.
I read the documentation and can't determine which of the following two is
correct if I want to get the sasa of the sidechains:

atomselect sidechain [atomselect top sidechain]
atomselect backbone [atomselect top backbone]

measure sasa 1.4 $sidechain -restrict $sidechain [1]
measure sasa 1.4 $sidechain -restrict $backbone [2]

If I want to the sasa of the sidechains which restrict selection is
correct, [1] or [2]?

Thanks,
Ed

On Mon, 7 Feb 2005, John Stone wrote:

>
> Ed,
> Since you're using b4, I think that the likely issue is that you
> need to add the restrict option to NOT count the surface area of
> atoms that border the parts you're excluding from the atom selection.
> The same would be true if you had internal cavities that you didn't want
> contributing to surface area.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Feb 07, 2005 at 12:49:18PM -0500, Edward Patrick Obrien wrote:
>> Hi John,
>> Thanks for the quick response.
>> The version is:
>> VMD for LINUX, version 1.8.3b4 (January 20, 2005)
>>
>> I've attached a graph of the time dependence of the sasa for
>> the protein, sidechains and backbone. I've checked several times
>> and I did not mislabel the files:)
>>
>> Ed
>>
>> PS- should I use the "restrict" option to correct this?
>>
>> On Mon, 7 Feb 2005, John Stone wrote:
>>
>>>
>>> Edward,
>>> Which exact beta version did you encounter this behavior with?
>>> We fixed a SASA calculation bug back in beta 3, so if you have a
>>> version older than that, that's the likely cause of the problem.
>>> Let me know which version you were testing with.
>>>
>>> Thanks,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Mon, Feb 07, 2005 at 12:26:16PM -0500, Edward Patrick Obrien wrote:
>>>> Hi All,
>>>> I downloaded the VMD v1.8.3 beta version to use the SASA command to
>>>> measure solvent accesible surface area.
>>>>
>>>> I can analyze my dcd's with it, BUT I am getting a physically
>>>> unreasonable result. The result is that the Surface area of the sidechains
>>>> is larger then the Surface area of the protein as a whole!!!
>>>>
>>>> The SA,protein = SA,sidechains + SA,backbone, should be true. But
>>>> instead I find:
>>>> SA,protein < SA,sidechains + SA,backbone
>>>>
>>>> with the SA,sidechains > SA,protein.
>>>>
>>>> My initial guess is the sasa command is not taking into account the
>>>> excluded volume of the backbone when it measures the surface area of the
>>>> sidechains, and vice-versa.
>>>>
>>>> Any suggestions about how to get self-consistent results?
>>>>
>>>> Thanks!
>>>> Ed
>>>>
>>>> PS- for srad I use 1.4, is this resonable?
>>>
>>> --
>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>>
>
>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>