VMD-L Mailing List

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Mon Feb 07 2005 - 12:47:34 CST

Hi John,
   I've tried to figure out how to define this "restricted selection"
correctly. I've one tentative conclusion, that I need you to confirm or
reject:

The restricted selection ("restrictedsel" according to documentation) MUST
be a subset of the "selection", to get the SASA of the "restrictedsel".

For example, to get the correct SASA of the sidechains (that is given
there is also a backbone that excludes some area), I define and measure
the sasa in the following manner:

vmd > set sidechain [atomselect top sidechain]
atomselect0
vmd > set backbone [atomselect top backbone]
atomselect1
vmd > set protein [atomselect top protein]
atomselect2

vmd > measure sasa 1.4 $protein -restrict $sidechain
1253.48669434
vmd > measure sasa 1.4 $protein -restrict $backbone
210.18057251

Is this correct? Please let me know your thoughts.

It is strange though, the unrestricted protein SASA is

vmd > measure sasa 1.4 $protein
1583.38793945

which still DOES NOT ADD UP from the components,
that is:

1583 is not equal to 1253+210.

Is this 8 percent difference acceptable?

Thanks,
Ed

PS- below are the transcripts of my atempts:

# Define the selections
vmd > set sidechain [atomselect top sidechain]
atomselect0
vmd >
vmd > set backbone [atomselect top backbone]
atomselect1
vmd > set protein [atomselect top protein]
atomselect2

# The unrestricted SASA
vmd > measure sasa 1.4 $protein
1583.38793945
vmd > measure sasa 1.4 $sidechain
1687.36560059
vmd > measure sasa 1.4 $backbone
759.833068848

# Incorrect, returns same SASA as unrestricted or 0
vmd > measure sasa 1.4 $sidechain -restrict $sidechain
1687.36560059
vmd > measure sasa 1.4 $sidechain -restrict $backbone
0.0
vmd > measure sasa 1.4 $sidechain -restrict $protein
1687.36560059
vmd > measure sasa 1.4 $backbone -restrict $sidechain
0.0

# Try a new selection
vmd > set bands [atomselect top "backbone and sidechain"]
atomselect5
vmd > measure sasa 1.4 $sidechain -restrict $bands
0.0
vmd > measure sasa 1.4 $bands -restrict $sidechain
0.0

# May be correct approach
vmd > measure sasa 1.4 $protein -restrict $sidechain
1253.48669434
vmd > measure sasa 1.4 $protein -restrict $backbone
210.18057251

On Mon, 7 Feb 2005, Edward Patrick Obrien wrote:

>
> 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
>>
>