Elaine, Many thanks for the comprehensive and succinct answer. Much appreciated George
On 7 Apr 2016, at 01:10, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, You probably don’t have to use the “protein&” parts if residues :1-125 are already just the amino acids, but I guess it doesn’t hurt.
A1 just means the area of a surface enclosing the first set of atoms in your command, A2 the area of a surface enclosing the second set of atoms in your command, A12 the area of a surface enclosing both sets of atoms together …
I tried to explain it in the docs and in this recent post: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012105.html>
I can’t shed any more light on the warning other than it said something was weird and thus to be aware that the numbers might not be reliable for that frame. Thus… the bad news is that you’ll probably run into surface calculation failures if you try to do this for every single frame in your trajectory. This “measure buriedArea” is generally applied to a single solved structure. The surface calculation is prone to numerical failure, and it’s more likely when a structure is less well packed or a bit distorted, as is more likely during MD. Although it didn’t fail, the results might be weird for that frame. I guess you can see how often you get a warning or failure. We have some suggested workarounds to surface failures but they are mainly for getting a surface display, not for area calculations, so not really useful in your situation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
I can’t guarantee that any will help, but here are a couple ideas of what you might do if you can’t run the calculation on every frame:
(A) if you have different trajectories for different ligands (or no ligand) try to get a single representative structure from each trajectory. This is easier said than done. You can do an “average” structure but a simple average is generally distorted. You might need to use some other software (not Chimera) to identify or produce a single average per trajectory, since I don’t think it would work very well to get the average in Chimera, even if you minimize it afterward. Minimizing in Chimera is slow and has limited ability to improve a moderately distorted structure.
Use navigation links on the left to see the “structure averaging” section: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/home/meng/docs/ContributedSoftware/minimize/minimize.html>
(B) cluster each trajectory and only run the calculation on the cluster representatives. That would at least be fewer calculations and thus a reduced chance of failure. See the “clustering” section: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
I hope this helps, Elaine
On Apr 6, 2016, at 2:18 PM, George Tzotzos <gtzotzos@me.com> wrote:
Hi Elaine,
Once again I’m thankful for your advice.
My intention is to measure the buried surface at the interface between the two protein subunits.
I used the command: measure buriedArea protein&:1-125 protein&:127-251
Compilation flags WARNING: check_SES_edge: weird case, 1 probe full1 and not full2 Buried solvent accessible surface area B1SAS = 568.796, B2SAS = 575.712, BaveSAS = 572.254 (A1 = 8050.38, A2 = 7571.28, A12 = 14477.2 = 7481.59 + 6995.57) Buried solvent excluded surface area B1SES = 230.525, B2SES = 278.114, BaveSES = 254.32 (A1 = 7326.4, A2 = 6934.86, A12 = 13752.6 = 7095.87 + 6656.74)
Could you please shed some light on what the warning actually means? Likewise on the meaning of A1, A2 and A12.
My last question (hopefully) is whether it is possible to get an average value over all frames of a given trajectory.
Thank you once again for your advice and help
George
On 5 Apr 2016, at 19:24, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, It doesn’t matter if the structure is from MD or an individual PDB… as long as you can show a molecular surface, then the SASA is automatically calculated and reported in the Reply Log. You can see from looking at the surface whether it included the ligand or not. If the ligand is outside of the surface, it is not included in the reported values in the Reply Log either. My guess is that it would not be lumped into the surface and so you would not need to strip it, but I suppose it depends on the details of your data.
But it sounds like you don’t want the SASA anyway, but the area that is buried between the chains. In that case skip down to part 2 of my answer below.
(1) After you show the surfaces of interest, solvent-excluded and solvent-accessible areas per atom and residue are assigned as attributes named areaSES and areaSAS, respectively. You can add up the per-atom or per-residue SASA for any sets of atoms or residues that you want (Tools… Structure Analysis… Attribute Calculator), but that will be in the context of the surface(s) already calculated. E.g. if you sum the surface areas of residues 12 and 13, but they are not exposed in the context of the surfaces that you are currently showing, the answer will be zero. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>
At least in some cases Chimera will not make separate surfaces for the monomers but instead group all the protein atoms into one surface. If you wanted separate surfaces, you could use “surfcat” to specify the specific sets of atoms you want in separate surfaces. For example:
surfcat one :.a&protein surfcat two :.b&protein surface one surface two
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>
(2) If you just want the interchain buried surface area, regardless of how the surface is displayed, you should instead use the “measure buriedArea” command and specify the two sets of atoms, e.g. if they are protein chains A and B:
measure buriedArea protein&:.A protein&:.B
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
If your MD data doesn’t have two different chain IDs but the monomers have different residue numbers, you could just give two residue-number ranges instead. 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 Apr 5, 2016, at 7:39 AM, George Tzotzos <gtzotzos@me.com> wrote:
I have a couple of questions on Chimera’s implementation of SASA. First, I’ll try to explain briefly my problem and then ask the questions.
My protein is a homodimer. There exist 3 X-ray structures of the protein in complex with serendipitous ligand as well as in complex with biological ones. The ligands bind at the interface between the two chains of the homodimer. It is not clear whether dimer formation is a crystallographic artefact. Biochemical experiments are likewise inconclusive. It has been argued that the biological ligands may stabilise the formation of the dimer. Furthermore, it has been argued that upon ligand binding some of the interface residues become buried.
I’ve conducted extensive MD simulations with and without the biological ligands. I would like to test whether ligand binding has an effect on the SASA of the interface residues.
1. Can I restrict measurement of SASA to selected residues only? In other words, can I use a mask specifying the residues of interest? 2. From the documentation, I understand that the Chimera implementation of SASA is applied on single pdb structures and not on trajectories. If I use representative structures from MD clusters, should I strip the ligand before measuring SASAs?
Thank you in advance for your suggestions and apologies for the long-winded explanation.
Best regards
George