FirstSurf<Atom|Res>

The FirstSurf command allows to separate surfaces that are not connected with each other but belong to the same object. Every protein has one main outer surface, and possibly a number of smaller inner surfaces, that enclose cavities. For each of these surfaces, the FirstSurf command returns the number of the first atom or residue contributing to the surface as well as the area of the surface.

The surfaces are sorted by size, with the main (=largest) surface returned first. Surfaces smaller than 1 A^2 are ignored.

In connection with the surface selection operators 'with distance from surface' and 'with contribution to surface', the FirstSurf command allows to restrict analysis to a subset of surfaces, e.g. only the main outside surface or a specific cavity of interest.

Like the Surf and ShowSurf commands, FirstSurf considers the current surface environment .

Example 1:

List the first atom contributing to each distinct accessible surface of object 1, as well as the areas of these surfaces.

Example 2:

Assign the number of the first atom contributing to the largest accessible surface in the soup to variable 'largest' and the area of this surface to 'area'.

Example 3:

Initialize 'firstsurflist' with the numbers of the first residue contributing to each distinct molecular surface in all proteins and the respective surface areas. Residue numbers get the odd list indices (1),(3).., surface areas the even indices (2),(4)..

# EXAMPLE FirstSurf # Requires YASARA Model # This macro writes all the surface information to log/surface_analysis.log # and shows all distinct surfaces as separate objects with the contributing # atoms in a different color Clear LoadPDB 5tim PosObj 1,3.3,0,22.3 OriObj 1,97,175,25.4 # Keep only the protein DelRes !Protein,Center=Yes # Make sure that residue numbers are unique RenumberRes all,2 HideAll StickAll # Perform analysis with solvent accessible surface surftype='accessible' SurfPar Probe=1.4,Resolution=3,Molecular=numeric surfareasum=0. # Get a list of the first atom in every distinct surface, plus the surface areas surflist() = FirstSurfAtom Protein,(surftype) surfaces = count surflist/2 # To extract partial surfaces, we need everything the entire protein in the environment AddEnvRes Protein # Print a summary Console Off RecordLog surface_analysis for i=1 to count surflist step 2 if i==1 Print 'Main surface:' if i==3 Print 'Secondary surfaces. If the protein does not contain fragments separate in space, these are all cavities:' # Get number of first atom at the surface and surface area from the list firstatom = surflist(i) surfarea = surflist(i+1) surfareasum = surfareasum+surfarea # Count how many atoms contribute to this surface surfselection = 'all with contribution to (surftype) surface touched by Atom (firstatom)' surfatoms = CountAtom (surfselection) # Get a list of all residues contributing to this surface reslist() = ListRes (surfselection) # Print surface summary Print ' Surface ((i+1)/2): (surfatoms) atoms contribute (0.0+surfarea) A^2 of (surftype) surface area.' text=" Residue numbers involved: " for res in reslist text=text+res+" " Print (text) # Now color and show the atoms ColorAtom (surfselection),((i-1)*180/surfaces) ShowAtom (surfselection) # And create a surface object obj=ShowSurfAtom (surfselection),(surftype),static,OutCol=AtomCol,OutAlpha=50,InCol=AtomCol,InAlpha=100 RenameObj (obj),'Surf((i+1)/2)' Print 'Sum of surface areas >1 A^2: (0.0+surfareasum) A^2.' surfarea = SurfAtom Protein,(surftype) Print 'Total surface area: (0.0+surfarea) A^2.' StopLog

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Get first surface atom(s) or residue(s) and area(s)

Example 1:

Example 2:

Example 3:

Example macro: