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Biological Small Angle Scattering |
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CORAL manualWritten by M.V. Petoukhov and D.I. Svergun. © ATSAS Team, 2009-2013 Table of ContentsManualThe following describes the method implemented in CORAL, details of the dialog prompt as well as the required input and the produced output files. CORAL combines the algorithms of SASREF
and BUNCH and is described by
Petoukhov, M.V., Franke, D., Shkumatov, A.V., Tria, G., Kikhney, A.G.,
Gajda, M., Gorba, C., Mertens, H.D.T., Konarev, P.V. and Svergun, D.I. (2012) IntroductionCORAL (COmplexes with RAndom Loops) performs SAXS-based rigid body modeling of complexes, one or several of whose components lack some fragments (e.g. termini portions or interdomain linkers are missing). CORAL, similarly to SASREF, translates and rotates the atomic models of individual domains belonging to multiple components of the complex, however these rearrangements are not fully random: the distances between the N- and C-terminal portions of the subsequent domains belonging to one chain are constrained. For this purpose a pre-generated library of self-avoiding random loops composed of DRs is utilized. It covers the linker lengths from 5 to 100 amino acids and samples 20 random structures for every possible end-to-end distances for the given length with the binning step of 2A. When a domain is moved in CORAL, its new position is examined by querying the library: if a linker of the appropriate length to connect this domain with preceding/following one cannot be found, then such a movement is rejected. If the query is successful, the corresponding random loop is inserted as a placeholder of the missing linker and its contribution is also added to the computed scattering intensity of the system and to the target function (e.g. overlaps, contacts restraints etc). C- and N- terminal portions can also be randomly selected from the library but they do not constrain the associated domain motion. CORAL allows one to simultaneously fit multiple scattering curves from the subsets of the entire system assuming the same arrangement of domains/subunits in these constructs. Also it allows taking symmetry (as constraint) and anisometry (as restraint) into account. A simulated annealing protocol is employed to find the optimal positions and orientations of available high resolution models of domains and the approximate conformations of the missing portions of polypeptide chain(s). Please refer to SASREF and BUNCH manuals and the paper cited above for the details of simulated annealing protocol, and the computation of the scattering intensity from a mixed model combining atomic resolution structures with DR chains. Running CORALInteractive ConfigurationCORAL can only be run in the dialog mode, no command line arguments are accepted. A special configuration file has to be created before running CORAL. There are two modes, EXPERT and USER. In the former mode, the users have the options to adjust any program parameters. In the latter mode, fewer questions are asked as the default values are used for the most of program parameters, the user only needs to provide basic input. The default settings are the same in both modes. CORAL interactive prompt:
Runtime OutputOn runtime, two lines of output will be generated for each temperature step: j: 1 T: 0.100E+01 Suc: 1000 Eva: 2711 CPU: 0.503E+02 F:30.8120 Pen: 28.0621 The best chi values: 1.65827 The fields can be interpreted as follows, top-left to bottom-right:
CORAL Input FilesCORAL uses the SAXS experimental data files (*.dat) in ASCII format containing 3 columns: (1) experimental scattering vector, (2) experimental intensity and (3) experimental errors. Starting configurationInitial configuration is specified using a configuration file which format is demonstrated by the example of a complex consisting of two proteins A and B (i.e. two chains), whereby A contains three domains a1.pdb, a2.pdb and a3.pdb, 20 aa are missing at the N-terminal and the two linkers are of 25 and 30 aa; B contains two domains b1.pdb and b2.pdb, 10 aa are missing at the C-terminal and the linker is of 15 aa: NTER 20 a1.pdb LINK 25 a2.pdb LINK 30 a3.pdb b1.pdb LINK 15 b2.pdb CTER 10 Note: any two pdb files not separated by the string LINK..., assumed to be belonging to different chains. If the symmetry is applied, the configuration should describe the asymmetric part only. ContactsAn optional contact conditions file has a format similar to that of SASREF with the only difference that it refers to the chains instead of subunits(domains). The following conditions require the distance of 7 Å between the residues 25 and 115 from the same chain and the distance of 5 Å between the residue 40 from the first chain and 50 from the second.
dist 7.0
1 25 25 1 115 115
dist 5.0
1 40 40 2 50 50
If two (or more) alternatives are given after the line with the keyword "dist", the program compares the better (smaller) distance among them with the specified one. CORAL Output FilesAfter each simulated annealing step, CORAL creates a set of output files, each filename starts with a customizable prefix that gets an extension appended. If a prefix has been used before, existing files will be overwritten without further note.
ExampleGlutamate decarboxylase (Gad) hexamer with three calmodulin (CaM) molecules bound to three pairs of Gad C-terminal peptides is employed for sample run. The structures of the homohexameric Gad core and 1:2 complex of CaM with C-terminal peptide are known. The peptide is connected to the Gad core domain by a 22 aa linker. The configuration file (config.con) is as follows:
m1.pdb
LINK 22
pept1a.pdb
m2.pdb
LINK 22
pept2a.pdb
cama.pdb
m3.pdb
LINK 22
pept1b.pdb
m4.pdb
LINK 22
pept2b.pdb
camb.pdb
m5.pdb
LINK 22
pept1c.pdb
m6.pdb
LINK 22
pept2c.pdb
camc.pdb
Here, m?.pdb and pept??.pdb are the atomic models of the Gad core domains and its C-terminal portions, respectively, and cam?.pdb are three copies of the CaM molecule. A listing of questions / answers of CORAL in USER mode:$ coral Computation mode (User or Expert) ...... < User >: Log file name .......................... < .log >: gadcam Project identificator .................................. : gadcam Enter project description .............. : Gad hexamer + 3 CaM Random sequence initialized from ....................... : 191723 File name with objects info ............ < .con >: config Coordinates of the 1-st subunit evaluated from ......... : m1.pdb 3512 atoms read, center at -30.70 -8.02 10.84 Fix the subunit at original position? [ Y / N ] < No >: Y Coordinates of the 2-nd subunit evaluated from ......... : pept1a.pdb 234 atoms read, center at -58.01 33.40 4.22 Fix the subunit at original position? [ Y / N ] < No >: Coordinates of the 3-rd subunit evaluated from ......... : m2.pdb 3512 atoms read, center at -8.40 30.59 -10.84 Fix the subunit at original position? [ Y / N ] < No >: Y Coordinates of the 4-th subunit evaluated from ......... : pept2a.pdb 234 atoms read, center at -66.51 30.35 8.17 Fix the subunit at original position? [ Y / N ] < No >: Coordinates of the 5-th subunit evaluated from ......... : cama.pdb 1170 atoms read, center at -67.64 33.48 -2.84 Fix the subunit at original position? [ Y / N ] < No >: Coordinates of the 6-th subunit evaluated from ......... : m3.pdb 3512 atoms read, center at 8.40 30.59 10.84 Fix the subunit at original position? [ Y / N ] < No >: Y Coordinates of the 7-th subunit evaluated from ......... : pept1b.pdb 234 atoms read, center at 57.93 33.53 4.22 Fix the subunit at original position? [ Y / N ] < No >: Coordinates of the 8-th subunit evaluated from ......... : m4.pdb 3512 atoms read, center at 30.70 -8.02 -10.84 Fix the subunit at original position? [ Y / N ] < No >: Y Coordinates of the 9-th subunit evaluated from ......... : pept2b.pdb 234 atoms read, center at 59.54 42.42 8.17 Fix the subunit at original position? [ Y / N ] < No >: Coordinates of the 10-th subunit evaluated from ........ : camb.pdb 1170 atoms read, center at 62.81 41.84 -2.84 Fix the subunit at original position? [ Y / N ] < No >: Coordinates of the 11-th subunit evaluated from ........ : m5.pdb 3512 atoms read, center at 22.29 -22.57 10.84 Fix the subunit at original position? [ Y / N ] < No >: Y Coordinates of the 12-th subunit evaluated from ........ : pept1c.pdb 234 atoms read, center at 0.07 -66.94 4.22 Fix the subunit at original position? [ Y / N ] < No >: Coordinates of the 13-th subunit evaluated from ........ : m6.pdb 3512 atoms read, center at -22.29 -22.57 -10.84 Fix the subunit at original position? [ Y / N ] < No >: Y Coordinates of the 14-th subunit evaluated from ........ : pept2c.pdb 234 atoms read, center at 6.97 -72.77 8.17 Fix the subunit at original position? [ Y / N ] < No >: Coordinates of the 15-th subunit evaluated from ........ : camc.pdb 1170 atoms read, center at 4.83 -75.32 -2.84 Fix the subunit at original position? [ Y / N ] < No >: Pair of domains to group .. < 0, 0 >: 2,4 Pair of domains to group .. < 0, 0 >: 2,5 Pair of domains to group .. < 0, 0 >: 4,5 Pair of domains to group .. < 0, 0 >: 7,9 Pair of domains to group .. < 0, 0 >: 7,10 Pair of domains to group .. < 0, 0 >: 9,10 Pair of domains to group .. < 0, 0 >: 12,14 Pair of domains to group .. < 0, 0 >: 12,15 Pair of domains to group .. < 0, 0 >: 14,15 Pair of domains to group .. < 0, 0 >: Number of backbone atoms generated ..................... : 3372 Averaged formfactors of DRs used DR formfactor multiplier ............................... : 1.000 Symmetry: P1...19 or Pn2 (n=1,..,12) ... < P1 >: Cross penalty .......................................... : 6.383e-2 Cross penalty weight ................................... : 100.0 Shift penalty .......................................... : 3.182e-3 Shift penalty weight ................................... : 1.000 File name, contacts conditions, CR for none < .cnd >: Input total number of scattering curves < 1 >: Input first & last residues in 1-st construct < 1, 3372 >: Enter file name, 1-st experimental data < .dat >: gad_cam-mer.dat Number of experimental points found .................... : 984 Angular units in the input file : 4*pi*sin(theta)/lambda [1/angstrom] (1) 4*pi*sin(theta)/lambda [1/nm ] (2) 2* sin(theta)/lambda [1/angstrom] (3) 2* sin(theta)/lambda [1/nm ] (4) < 1 >: Fitting range in fractions of Smax ..... < 1.000 >: Experimental radius of gyration ........................ : 57.80 Number of points in the Guinier Plot ................... : 10 Maximum s-vector in master grid ........................ : 0.4478 Number of points in partial amplitudes ................. : 101 Maximum order of harmonics ............................. : 14 Computing X-ray Alms for m1.pdb ALMGRZ --- : 181800 summation coefficients used Computing X-ray Alms for pept1a.pdb Computing X-ray Alms for m2.pdb Computing X-ray Alms for pept2a.pdb Computing X-ray Alms for cama.pdb Computing X-ray Alms for m3.pdb Computing X-ray Alms for pept1b.pdb Computing X-ray Alms for m4.pdb Computing X-ray Alms for pept2b.pdb Computing X-ray Alms for camb.pdb Computing X-ray Alms for m5.pdb Computing X-ray Alms for pept1c.pdb Computing X-ray Alms for m6.pdb Computing X-ray Alms for pept2c.pdb Computing X-ray Alms for camc.pdb Total penalty .......................................... : 6.386 1-st curve: NEXP reduced to ........................................ : 983 Theoretical points from 5 to 101 used The best chi values:11.03272 Initial fVal ........................................... : 128.1 Spatial step in angstroems ............. < 5.000 >: Spatial step in angstroems ............. < 5.000 >: Angular step in degrees ................ < 20.00 >: Initial annealing temperature .......................... : 10.00 Annealing schedule factor .............................. : 0.9000 Max # of iterations at each T .......................... : 51600 Max # of successes at each T ........................... : 5160 Min # of successes to continue ......................... : 100 Max # of annealing steps ............................... : 100 ==== Simulated annealing procedure started ==== j: 1 T: 0.100E+02 Suc: 1000 Eva: 1165 CPU: 0.107E+03 F:15.8416 Pen: 1.2895 The best chi values: 3.81472 j: 2 T: 0.900E+01 Suc: 1000 Eva: 2337 CPU: 0.214E+03 F:15.8416 Pen: 1.2895 The best chi values: 3.81472 j: 3 T: 0.810E+01 Suc: 1000 Eva: 3477 CPU: 0.317E+03 F:14.4729 Pen: 1.9555 The best chi values: 3.53799 ... Note that the six core domains of Gad are fixed so that the hexamer remains intact and three CaM are coupled with two C-terminal peptides each to keep their known arrangement. |
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Last modified: April 11, 2013
© BioSAXS group 2013