[Chimera-users] SASA vs. MSA
meng at cgl.ucsf.edu
Sun Aug 5 09:58:06 PDT 2012
Note the atoms might not be in the same order in your written lists. The hydrogens might be at the bottom of one list.
The more direct way to check how many atoms are selected is to use selection commands like in my example, then click the magnifying glass icon on the lower right corner of the Chimera window to open the Selection Inspector.
On Aug 5, 2012, at 9:55 AM, Elaine Meng wrote:
> Hi Nikolay,
> The first thing would be to check that you made both lists after adding the hydrogens, of course. Personally I do not do not add hydrogens before area calculations.
> You could reopen the structure, do not add hydrogens, show surface, and make your lists again.
> If your lists are truly based on all atoms with area >0 the same atoms (plus or minus a very few from rounding issues) should be listed for SAS and SES. Please test that first using the commands in my previous message.
> You can do various experiments selecting with similar commands but different cutoffs.
> If you still think something is wrong you could use Help... Report a Bug, explain what you think is wrong, and attach the structure file exactly in the same state as when you made the measurements. It is no use to waste time speculating without seeing the exact data.
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Aug 5, 2012, at 9:45 AM, Nikolay Igorovich Rodionov wrote:
>> Thanks Elaine,
>> One thing I noticed when I was looking at the raw data lists form SES and SAS atoms is that there were no Hydrogens present in the SAS list but they were frequent on the SES list.
>> Can you explain this?
>> -----Original Message-----
>> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
>> Sent: Sunday, August 05, 2012 12:29 PM
>> To: Nikolay Igorovich Rodionov
>> Cc: chimera-users at cgl.ucsf.edu BB
>> Subject: Re: [Chimera-users] SASA vs. MSA
>> Hi Nikolay,
>> I suspect you may be using a cutoff value for this comparison, which may be giving a false impression.
>> I believe the sets of atoms contributing to MS (SES) and SAS should be the same, based on the definitions of these surfaces (see Fig 3 in http://ieeexplore.ieee.org/ieee_pilot/articles/06/ttg2009061391/figures.html ).
>> I.e., these commands should select the same or very nearly the same numbers of atoms:
>> sel @/areaSAS>0
>> sel @/areaSES>0
>> However, if you are looking at contributions to SES and SAS >N square angstroms where N>0, because the SAS is farther out from the atomic centers and thus larger in magnitude, that will select more atoms for SAS.
>> VDW radius is irrelevant to this comparison since the SES and SAS calculations are based on the same set of atomic radii.
>> I hope this clarifies things,
>> On Aug 4, 2012, at 9:09 PM, Nikolay Igorovich Rodionov wrote:
>>> Hi all,
>>> I was wondering if you could help me conceptualize what is going on in this situation. I ran both solvent accessible surface area and solvent excluded (molecular) surface area calculations. When I compared the output for both of these calculations I found that, overall, atoms that contribute to the SASA are buried 1-3 angstroms deeper in the protein than those that contribute to the MSA.
>>> I don't really understand how this could be unless the deeper buried SASA atoms have a much larger van der waals radii than MSA atoms (I get that some atoms contribute to both).
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>>> Chimera-users at cgl.ucsf.edu
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