[Chimera-users] User Inquiry

[Yen Bui]

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


On Jun 25, 2012, at 2:15 PM, Yen Bui wrote:

> To whom this may concern,
>
> I’m an undergraduate student doing some research at KSTATE this summer and I’ve been assigned to work on a project that utilizes Chimera.
>
> My professor is unavailable a lot of the time and I’ve been struggling a bit with a problem.
>
> I’ve been successful at opening up the following PDB files:
>
> 1DHK     1DPX       1HYL       2CAU       3BLG      1OA6       1JBC      1OA5
>
> I’m able to open up the .pdb files, proceed to use the commands “del solvent” and “del @ .b” in the command line.
>
> I’m also able to go to ToolsàHigher Order Structure à Crystal Contacts before changing the contact distance from 1.0 to 4.0 and check mark the create copies of contacting molecules.
>
> However when I attempt to do the following actions for the rest of the proteins I run into a variety of issues:
>
> For example 2CAU:
>
> When I attempt to “measure buried area #0 # 2-7,” I get the following response in my reply log:
>
> #0, chain A: JACK BEAN vicilin
>
> 6 pairs of NCS asymmetric units of 2CAU contact at distance 1.0 A
>
>   Atoms              MTRIX            SMTRY            Unit cell           MTRIXref           Copies
>
>       1                      0                     4                 0  0  0                  0                       1
>
>       1                      0                     5                 0  0  0                  0                       1
>
>       1                      0                     6                 -1  0 -1                  0                       1
>
>       1                      0                     8                 0  0  0                  0                       1
>
>       1                      0                     9                 0  0 -1                  0                       1
>
>       1                      0                    11                0  0 -1                  0                       1
>
> C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1
>
> MSMSLIB 1.3 started on Local PC
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
> C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1
>
> MSMSLIB 1.3 started on Local PC
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
> C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1
>
> MSMSLIB 1.3 started on Local PC
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
> C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0
>
> MSMSLIB 1.3 started on Local PC
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
> C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0
>
> MSMSLIB 1.3 started on Local PC
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
> C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0
>
> MSMSLIB 1.3 started on Local PC
>
>
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
> C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0
>
> MSMSLIB 1.3 started on Local PC
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags [End of Reply Log]
>
> So I’m not able to get back the calculations I want.
>
> Also, when I attempt to use the Surface Analysis à Attributes Calculator to run the following function : sum(atom.buriedSASArea) and check the “Restrict formula domain to current selection, if any”  and “Save calculation results to file,” after selecting the “C” atoms I get the reply:
>
>  Formula evaluation error: expecting vector argument in function
>
> Is there something I need to do before I attempt these actions?
>
> Also, I have very little experience with programs in general (I’m a chemistry major/upcoming experimental chemist working with theortical physicist…a little out of my element).
>
> Thanks in advance,
>
> -Yen Bui