[Chimera-users] Calculating AreaSES/AreaSAS without a molecular surface?

Tom Goddard goddard at sonic.net
Wed Sep 27 11:57:08 PDT 2017


Hi Oliver,

  ChimeraX does not yet have coloring by atom attributes and the “measures sasa” command isn’t saving a per-atom attribute.  But you could tweak the code a bit and get the values in the bfactor column of a PDB file.  For instance, I added two lines to the ChimeraX Python code for measure sasa in file

	ChimeraX.app/Contents/lib/python3.6/site-packages/chimerax/core/commands/measure_sasa.py

after line 32

    areas = spheres_surface_area(atoms.scene_coords, r)

add two lines that set the atom bfactor

    areas = spheres_surface_area(atoms.scene_coords, r)
    for a, ar in zip(atoms, areas):
        a.bfactor = ar

Then use the command “save areabfactors.pdb” to get those area values in the bfactor column.  Some day we will putting the Chimera rangecolor command into ChimeraX so coloring and measure sasa will set an atom attribute enabling the coloring in ChimeraX without code tweaks.

	Tom


> On Sep 27, 2017, at 11:42 AM, Oliver Clarke wrote:
> 
> Hi Tom,
> 
> Thanks! But ChimeraX doesn’t assign it as a per-residue attribute, or am I missing something?
> 
> Is there any way to write out that parameter in ChimeraX per residue or atom, e.g. by replacing the B-factor column?
> 
> Cheers
> Oli
> 
>> On Sep 27, 2017, at 2:37 PM, Tom Goddard  wrote:
>> 
>> Hi Oliver,
>> 
>> The Chimera solvent accessible and solvent excluded surface area calculations are done by the MSMS surface calculation code, so if it fails you cannot get those numbers.  The secret “grid” option in Chimera does not allow computing areas.
>> 
>>  ChimeraX computes the areas analytically (command “measure sasa”) and does not create a surfaces (and the ChimeraX surface calculation never fails).
>> 
>> 	Tom
>> 
>> 
>>> On Sep 27, 2017, at 11:20 AM, Oliver Clarke wrote:
>>> 
>>> Hi,
>>> 
>>> Is it possible to calculate the areaSES/areaSAS attributes without a molecular surface? For most large complexes, it is only possible to calculate surfaces using the `grid option` (because msms fails), but this does not automatically generate the SES/SAS attributes.
>>> 
>>> Cheers
>>> Oli
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>>> 
>> 
> 
> 




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