[Chimera-users] Measuring SASA of ligand

Wed Nov 9 14:53:51 PST 2016

Most grateful for the clarifications Elaine. Indeed the select command picks up the correct elements.

Have a good evening

George

> On 9 Nov 2016, at 23:49, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi George,
> The assignments of chain ID are not relevant since you are not specifying by chain ID.  You were specifying as “protein”.  Also, whether “ligand” and “protein” are recognized are not exactly the point, you should check by using the “select" command that they select everything you expect and nothing else, e.g. see what happens with
> 
> select ligand
> select protein
> 
> The warning is what I mentioned, that the surface calculation may fail on some trajectory frames, and thus I would not use the values from those frames.
> 
> Also I think you did not read the results correctly… if you specified the ligand first (if :126 is the ligand), then B1SAS is its buried solvent-accessible surface area and A1 is its total area.  Thus in the protein monomer, 324 of 402 square Ang total of the ligand are buried, and in the protein dimer, 396 of 406 total of the ligand are buried, assuming that the values were not invalidated by surface calculation failure. If you specfied the ligand second, then B2SAS is its buried solvent-accessible surface area and A2 is its total area.
> 
> I hope this helps,
> 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 Nov 9, 2016, at 2:32 PM, George Tzotzos <gtzotzos at me.com> wrote:
> 
>> Hi Elaine,
>> 
>> As always “quick on the ball” and extremely helpful.
>> 
>> I followed your suggestions for the first snapshot of each trajectory. 
>> 
>> I got the following Chimera Warning “Calculation of some surface components failed. Using only single surface component. This may give inaccurate areas if surfaces of either set of atoms or the combined set are disconnected”.  
>> 
>> How important is this?
>> 
>> Other than that, from the reply log, it seems that the protein and ligand are recognised. Here’s a summary of the log:
>> 
>> 1. Monomer. Command: measure buriedArea :126 protein
>> 
>> Assigning chain ID A to 125 residues, e.g. ASP # correct. The monomer has 125 residues
>> Model 0 (prod_100ns.nc) appears to be a protein without secondary structure assignments.
>> 
>> Several WARNINGS
>> 
>> Calculation of some surface components failed.  Using only single surface component.  This may give inaccurate areas if surfaces of either set of atoms or the combined set are disconnected.
>> 
>> Buried solvent accessible surface area
>>  B1SAS = 324.016, B2SAS = 223.111, BaveSAS = 273.564
>>  (A1 = 401.975, A2 = 8118.7, A12 = 7973.55 = 77.959 + 7895.59)
>> Buried solvent excluded surface area
>>   B1SES = 96.114, B2SES = 177.797, BaveSES = 136.955
>>  (A1 = 207.413, A2 = 7117.15, A12 = 7050.65 = 111.299 + 6939.35)
>> 
>> 2. Dimer. Command: measure buriedArea :126 protein
>> 
>> Assigning chain ID A to 125 residues, e.g. ASP
>> Assigning chain ID B to 125 residues, e.g. ASP
>> # above assignment of chains is correct
>> 
>> Several WARNINGS
>> 
>> Buried solvent accessible surface area
>>  B1SAS = 395.601, B2SAS = 202.981, BaveSAS = 299.291
>>  (A1 = 405.778, A2 = 14917.3, A12 = 14724.5 = 10.1763 + 14714.3)
>> Buried solvent excluded surface area
>>   B1SES = 169.315, B2SES = 300.475, BaveSES = 234.895
>>  (A1 = 208.956, A2 = 13673.7, A12 = 13412.9 = 39.6405 + 13373.3)
>> 
>> If I read the above correctly, the buried solvent accessible area for the ligand in the monomer complex is ~ 78 angstrom and for the ligand in the dimer complex ~ 10 angstrom.
>> 
>> Many many thanks for your kind help
>> 
>> George
>> 
>>> On 9 Nov 2016, at 22:40, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi George,
>>> That earlier post is probably not that relevant to your situation.  I’ll try to outline what you might try.  First you would need to figure out command-line specifications that work on your trajectories, for:
>>> 
>>> (1) the ligand - sometimes “ligand” will work, but not always, as that might also include other stuff you don’t want like sulfate ions.  Just check with “sel ligand” and see if that is the only thing that gets selected.  Otherwise you might need to use its residue name or number, e.g. :HEM or :128
>>> 
>>> (2) the protein monomer in one trajectory - “protein” might work but you should check to make sure that it selects everything you want and nothing else.  If not, you may need to use a residue number range instead.
>>> 
>>> (3) the protein dimer in the other trajectory - again “protein” might work
>>> 
>>> Once you’ve figured out those things, let’s call them spec1, spec2, and spec3, you can try out the buriedArea command on some single frame of the trajectory.  For the first trajectory, command:
>>> 
>>> measure buriedArea spec1 spec2
>>> … for example:
>>> measure buriedArea ligand protein
>>> 
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
>>> 
>>> … and for the second trajectory, measure buriedArea spec1 spec3.  If the command works (you see plausible results in Reply Log), then you could put the command in a per-frame script in MD Movie to have it run at every frame.  The results in the Reply Log will include the area of the two things together and each individually, as well as the resulting buried area, and two sets of results, one for SES (solvent-excluded surface) and one for SAS (solvent-accessible surface).  You may have used a per-frame script before for H-bond calculations.  
>>> 
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
>>> 
>>> One problem is that sometimes the surface calculation may fail, especially during dynamics.  You may not be able to get results for every frame, so it is probably good to have the script echo frame number into the Reply Log so you can be sure about which results you are getting.  In other words, the per-frame command script could include a command like:
>>> 
>>> echo frame # <FRAME>
>>> 
>>> I hope this helps,
>>> 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 Nov 9, 2016, at 12:10 PM, George Tzotzos <gtzotzos at me.com> wrote:
>>> 
>>>> I’m dealing with two separate trajectories involving:
>>>> 
>>>> 1. Ligand A in complex with the monomeric subunit of a given protein A
>>>> 2. the same ligand in complex with the dimer of protein A
>>>> 
>>>> I would like to measure the buried (or solvent accessible) surface area of ligand A in both cases.
>>>> 
>>>> I referred to a relevant posting in the list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012472.html) but I’m not sure how this could apply in the above case. 
>>>> 
>>>> I’d be grateful for any suggestion on how to deal with this type of measurement.
>>>> 
>>>> Many thanks in advance for any suggestions
>>>> 
>>>> George
>>>> 
>>>> 
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>>> 
>> 
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