[Chimera-users] User Inquiry

[Elaine Meng]

I would take the messages literally, and yes, as a result the numbers you get may not be correct.  That's why it is warning you!  The August 2009 link in my previous message (below) contains some discussion about whether the buried area results could still be right in some cases.

I believe the "split" suggestion, while relevant to surface display in general, is not really relevant to the buried area calculation.

The attribute calculator says it can't calculate attribute for one molecule, so in that case you wouldn't get a value for that attribute for that molecule model. If there were other molecule models, this wouldn't affect them (although of course you would need correct input values for your output to be correct).

B1SAS and B2SAS are just the changes in SAS (alone vs. in complex) for each of the two groups of atoms separately. If you are measuring buried area between C and D, one is the change in surface area of C and the other is the change in surface area of D.

Elaine

On Jul 2, 2012, at 12:02 PM, Yen Bui wrote:

> Dear Dr. Meng,
> 
> I did as you directed and was able to get the attribute calculator to work and  the buried surface area measured. 
> 
> However for a couple of proteins, after I was given the buriedSASArea, I was notified that:
> 
> “Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface.  If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed.”
> 
> Or 
> 
> “Calculation of some surface components failed.”
> 
> Should I be concerned about the measurement of the area or should I just ignore this warning? 
> 
> Also, after attempting to use the attribute calculator I was notified that the program was:
> 
> “Unable to calculate attribute for one molecule.”
> 
> Should I worry about this also? I’m given values, but I’m not sure about how accurate they are or if there’s anything I can do to check (I’m not sure how to split the protein either). 
> 
> Also, what is the different between B1SAS and B2SAS? Are they just two measurements brought about by two different methods of measuring the buried surface area?
> 
> 
> ________________________________________
> From: Elaine Meng [meng at cgl.ucsf.edu]
> Sent: Monday, June 25, 2012 11:25 PM
> To: Yen Bui
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] User Inquiry
> 
> Hi Yen,
> Two issues, one easily fixed and other, perhaps not.
> 
> (1) with the attribute calculator, you just need to make the new attribute to be for "models" instead of for "atoms" (using the little menu near the top right of the dialog), because you just want one value for the whole model, which is the sum over the selected atoms.
> 
> However.... there may not be a "buriedSASArea" value available due to the second problem...
> 
> (2) this is not your own error, but because the MSMS surface calculation fails numerically on some structures.  The buried area calculation requires the MSMS surface calculation to work.  There are some tricks to try to make the surface calculation work, but they may not apply to the buried area calculation, and there is no "rule" that a certain trick will always work.  For the buried area calculation, some possibilities to try are (a) changing MSMS calculation parameters beforehand in the Preferences, category: New Surfaces (Preferences are under Favorites in the menu), or (b) deleting any extra chains that are not involved in the calculation of interest.  It might not be possible to find settings that work for your structure, however.
> 
> The MSMS failures have been discussed in many posts to chimera-users, for example see
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-August/004195.html>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html>
> 
> One way to see if the buriedSASArea and buriedSESArea attributes exist is to look in the Render by Attribute tool (in menu under Tools... Structure Analysis).  With this tool you can also color the atoms to show the values and see if they make sense.
> 
> Best wishes in your work,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>