Gyration radius calculation device, system, method and program

Abstract

To provide a gyration radius calculation device, system, method and program for calculating a radius of gyration for a polymer in a solution that has a dynamically varying structure as a final calculated value.SOLUTION: A gyration radius calculation device for calculating a radius of gyration for a polymer molecule in solution includes an electron density map generation unit that generates multiple electron density maps from the actual X-ray scattering profile obtained by measuring the sample, and a theoretical size calculation unit that creates a plot of a dynamic radius of rotation of the molecule calculated based on the multiple electron density maps for each of multiple voxel sizes as a second plot, and calculates an extrapolated value at which the voxel size becomes zero on a regression line of the second plot as a final calculated value of the dynamic radius of rotation of the molecule.SELECTED DRAWING: Figure 9

Description

[Technical field]

[0001] The present invention relates to an apparatus, system, method and program for determining a three-dimensional electron density map of a polymer in a solution. [Background technology]

[0002] There has been much research into methods for observing biopolymers in solution. When X-rays are irradiated onto a biopolymer that is moving freely in a solution, ring-shaped scattered light is generated instead of a spot. There is a known technology for detecting this scattered light and obtaining a three-dimensional electron density map of the target molecule from the obtained measured X-ray scattering profile (Non-Patent Document 1).

[0003] The method described in Non-Patent Document 1 represents a cubic volume in real space containing particles as cubic voxels discretized into an N x N x N grid, and calculates an electron density map by iteratively searching for structure factors based on X-ray scattering data obtained from the sample. [Prior art documents] [Non-patent literature]

[0004] [Non-Patent Document 1] Thomas D Grant, "Ab initio electron density determination directly from solution scattering data", Nature Methods volume 15, 29 January 2018, pages191-193 Summary of the Invention [Problem to be solved by the invention]

[0005] However, the method described in Non-Patent Document 1 can only obtain an electron density map that is an average of multiple structures. Therefore, when analyzing the shape of a rigid molecule, a valid electron density map is calculated, but in the case of a flexible molecule, the dynamic molecular shape is averaged and the electron density that should be obtained is not calculated.

[0006] The present invention has been made in consideration of the above circumstances, and aims to provide an electron density map specifying device, system, method, and program that can reproduce the electron density map of a polymer in a solution that has a structure with dynamic fluctuations. [Means for solving the problem]

[0007] (1) In order to achieve the above-mentioned object, the electron density map identifying device of the present invention is an electron density map identifying device that identifies an electron density map of a polymer in a solution, and is characterized by comprising: an electron density map generating unit that generates a plurality of electron density maps from a measured X-ray scattering profile obtained by measuring a sample; an index calculating unit that calculates an index representing a degree of agreement between a calculated X-ray scattering profile calculated from each of the plurality of electron density maps and the measured X-ray scattering profile; and an electron density map selecting unit that selects a representative electron density map from the plurality of electron density maps based on the calculated index.

[0008] (2) Furthermore, the electron density map identifying device described in (1) above further includes a correlation determining unit that creates a first plot of a parameter representing a molecular size versus the calculated index for each of the plurality of electron density maps and determines whether or not there is a correlation in the first plot, and the electron density map selecting unit does not select the representative electron density map when there is no correlation in the first plot.

[0009] (3) Furthermore, the electron density map identification device described in (2) above is characterized in that it further includes a trend analysis unit that performs multivariate analysis on the distribution of the first plots when there is no correlation between the first plots, and the electron density map generation unit generates the multiple electron density maps by changing conditions when there is a trend in the distribution of the first plots.

[0010] (4) Furthermore, in the electron density map identifying device described in (2) above, the correlation determination unit creates the first plot when there is no correlation with the first plot, and the electron density map generation unit generates the multiple electron density maps under conditions based on instructions from a user.

[0011] (5) Furthermore, in the electron density map identification device described in any one of (1) to (4) above, the electron density map generation unit generates each of the multiple electron density maps one by one through repetitive processing in accordance with settings.

[0012] (6) Furthermore, in the electron density map identification device described in any one of (1) to (4) above, the electron density map generation unit is characterized in that it generates each of the multiple electron density maps at once by parallel processing in accordance with settings.

[0013] (7) In addition, the electron density map identification device described in any one of (1) to (6) above further includes a theoretical size calculation unit that creates a second plot of a parameter representing the calculated molecular size versus voxel size for each of the multiple electron density maps and calculates a calculated value of a parameter representing the molecular size of the polymer in the solution using the second plot, and an actual size calculation unit that calculates an actual value of the parameter representing the molecular size of the polymer in the solution from the actual X-ray scattering profile, and is characterized in that the electron density map selection unit does not select the representative electron density map unless a difference between the calculated value and the actual value is within a predetermined range.

[0014] (8) The system of the present invention further comprises an X-ray solution scattering apparatus and an electron density map determination apparatus described in any one of (1) to (7) above, wherein the electron density map determination apparatus determines an electron density map of a polymer in the solution based on an X-ray scattering profile of the polymer in the solution measured by the X-ray solution scattering apparatus.

[0015] (9) Furthermore, a method of the present invention is a method for identifying an electron density map of a polymer in a solution, and is characterized by including the steps of: generating a plurality of electron density maps from an actual X-ray scattering profile obtained by measuring a sample; calculating an index representing a degree of agreement between a calculated X-ray scattering profile calculated from each of the plurality of electron density maps and the actual X-ray scattering profile; and selecting a representative electron density map from the plurality of electron density maps based on the calculated index.

[0016] (10) Furthermore, a program of the present invention is a program for identifying an electron density map of a polymer in a solution, and is characterized in that it causes a computer to execute the following processes: generating a plurality of electron density maps from an actual X-ray scattering profile obtained by measuring a sample; calculating an index representing a degree of agreement between a calculated X-ray scattering profile calculated from each of the plurality of electron density maps and the actual X-ray scattering profile; and selecting a representative electron density map from the plurality of electron density maps based on the calculated index. [Brief description of the drawings]

[0017] [Figure 1] FIG. 1 is a schematic diagram showing a system of the present invention. [Diagram 2] FIG. 2 is a perspective view showing an X-ray solution scattering device. [Diagram 3] 1 is a block diagram showing a system of the present invention; [Figure 4] 4 is a flowchart showing the operation of the electron density map specifying device of the present invention. [Diagram 5] 1 is a graph showing an example of an X-ray scattering profile. [Figure 6] FIG. 2 is a schematic diagram showing an electron density map. [Figure 7] Graphs showing (a) and (b) the ideal distribution and the unanalyzable χ2-Rg(ind) distribution, respectively. [Figure 8] 1 is a graph showing the distribution of Rg(ind) versus χ2 in an embodiment. [Figure 9] 13 is a graph showing the extrapolation of Rg(sect) versus voxel size in an embodiment. [Figure 10] 1 is a list showing an electron density map and processing results in an embodiment. [Figure 11] (a) to (c) are front, top, and right side views showing selected electron density maps, respectively. To aid in understanding the obtained electron density maps, a structural ribbon model obtained by separate X-ray crystal structure analysis is superposed. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0018] Next, an embodiment of the present invention will be described with reference to the drawings. In order to facilitate understanding of the description, the same reference numerals are used to refer to the same components in each drawing, and duplicated description will be omitted.

[0019] [Electron density map identification system] FIG. 1 is a schematic diagram showing an electron density map determination system 10. The electron density map determination system 10 includes an X-ray solution scattering device 100 and an electron density map determination device 200. The X-ray solution scattering device 100 measures an X-ray solution scattering profile by irradiating a sample S0 with X-rays and detecting the scattered X-rays. The sample S0 is suitable for a polymer in a solution, particularly a biopolymer. The sample S0 may be a pharmaceutical molecule, a molecular complex or a structure in a solution. In addition, by using the X-ray solution scattering method, it is possible to visualize the electron density corresponding to an ensemble of structures of biopolymers that cannot be observed in a frozen or crystalline state.

[0020] The electron density map specifying device 200 is composed of a computer 210, an input device 280, and an output device 290, and controls the operation of the X-ray solution scattering device 100, and also acquires and processes measurement data from the X-ray solution scattering device 100.

[0021] The X-ray solution scattering device 100 includes an X-ray generation unit 110, a sample loading mechanism 120, a detector 130, and a control unit 140. The X-ray generation unit 110 has an X-ray source 111 and irradiates the sample S0 with X-rays. The sample loading mechanism 120 sends out "a polymer or a solution excluding only the polymer, which is a sample accompanied with a solution" to an X-ray irradiation position. The detector 130 detects the X-rays scattered by the sample S0 and transmits the obtained measurement data to a computer 210.

[0022] The computer 210 is, for example, a PC, and is composed of a processor that executes processing, and a memory or a hard disk that stores programs and data. The computer 210 receives user input from an input device 280 such as a keyboard or a mouse. Meanwhile, the computer 210 displays plots, visualized electron density maps, input screens, and the like on an output device 290 such as a display. The computer 210 may be a server device placed on a cloud. In addition, in terms of processing load, the function of controlling the operation of the X-ray solution scattering device 100 and the function of processing the measurement data may be separated, and the control may be performed by a PC installed on-site, and the data processing may be performed by a server device.

[0023] [X-ray solution scattering device] FIG. 2 is a perspective view showing an X-ray solution scattering apparatus 100. The X-ray solution scattering apparatus 100 includes an X-ray source 111, an optical system 115, a Kratsky block 117, a sample holding tube 125, and a detector 130. The X-ray source 111 is a line radiation source or a point radiation source, and emits a diverging beam. The optical system 115 is, for example, a KB parallel type or serial type optical system. The pair of Kratsky blocks 117 interact with the X-rays by their respective edges to define one side and the other side of the X-ray beam. This makes it possible to remove parasitic scattering from the irradiated X-rays. The sample holding tube 125 delivers and holds a solution sample of 1 μl to 20 μl. The detector 130 detects the X-rays scattered by the solution sample.

[0024] [Electron density map identification device] 3 is a block diagram showing the electron density map determination system 10. The electron density map determination device 200 acquires data of an X-ray scattering profile measured by the X-ray solution scattering device 100, and determines an electron density map of a polymer based on the data. The functions of the electron density map determination device 200 are mainly realized by a computer 210.

[0025] The computer 210 includes an input / output control unit 211, a measurement control unit 215, a measurement data storage unit 217, an electron density map generation unit 221, a theoretical scattering intensity calculation unit 225, an index calculation unit 226, a correlation determination unit 231, a trend analysis unit 232, a theoretical size calculation unit 245, an actual size calculation unit 246, a comprehensive determination unit 257, and an electron density map selection unit 258. Each unit can transmit and receive information via a control bus L.

[0026] The input / output control unit 211 receives input from the input device 280 and controls output to the output device 290. The input / output control unit 211 can, for example, receive input of measurement conditions and receive input of conditions for generating multiple electron density maps. The input / output control unit 211 can also output various plots and output electron density maps of identified polymers.

[0027] The measurement control section 215 controls the operation of the X-ray solution scattering apparatus 100. The control includes sending out the sample, generating X-rays, and moving the sample position and the detector. The control instructions are sent to the control unit 140 in the X-ray solution scattering apparatus 100, which controls each part of the X-ray solution scattering apparatus 100.

[0028] The measurement data storage unit 217 stores the measurement data of the X-ray solution scattering profile detected by the X-ray solution scattering device 100. The stored measurement data is used to generate an electron density map, calculate an index, and calculate the actual measured value of the molecular size of a polymer.

[0029] The electron density map generating unit 221 generates a plurality of electron density maps from an actual X-ray scattering profile obtained by measuring the sample S0. The generation of the electron density maps will be described in detail later.

[0030] From the obtained electron density map, the calculated value of the dynamic radius of gyration of the electron density map representing the target molecule, Rg(ind), and an index χ indicating the degree of agreement between the measured data and the calculated scattering curve for each electron density map are obtained. 2 and plotting them to create a first plot (see FIG. 8 described later). The dynamic radius of gyration Rg of a molecule is a suitable example of a parameter representing the molecular size, and other parameters representing the molecular size may also be used.

[0031] It is preferable that the electron density map generating unit 221 generates a plurality of electron density maps by changing conditions when there is a trend in the distribution of the first plot. This makes it possible to try to regenerate an electron density map when none of the electron density maps are valid. The electron density map generating unit 221 can also generate a plurality of electron density maps under conditions based on a user's instruction. This makes it possible to try to generate an electron density map by changing conditions when none of the electron density maps are valid.

[0032] The electron density map generating unit 221 can generate each of the multiple electron density maps one by one by repeated processing according to the settings. This makes it possible to allocate necessary computational resources and proceed with the processing while suppressing unnecessary processing and checking the validity of the electron density map. The electron density map generating unit 221 may also generate each of the multiple electron density maps at once by parallel processing according to the settings. This makes it possible to reproduce an electron density map of a biopolymer with high validity in a short time.

[0033] The index calculation unit 226 calculates an index that indicates the degree of agreement between the calculated X-ray scattering profile calculated from each of the multiple electron density maps and the actually measured X-ray scattering profile. Specifically, the index that has been subjected to statistical processing is χ 2 However, there is no particular limitation as long as it is an index showing the degree of agreement with the X-ray scattering profile. 2 Other than that, there are parameters of normal distribution or Poisson distribution, R value, RMS value and RMD value, which are indices that indicate the degree of agreement between the structure factor calculated from the measured diffraction data and the structure factor based on the electron density obtained by analysis. 2 can be calculated as follows:

[0034]

number

[0035] The correlation determination unit 231 creates a first plot by plotting a parameter representing the molecular size against the calculated index for each of the multiple electron density maps, and determines whether or not there is a correlation in the first plot. It is preferable that the correlation determination unit 231 creates a first plot that can be output and displays the first plot on a display. This allows the user to visually check whether or not there is a correlation in the first plot.

[0036] When performing repeated processing, the correlation determination unit 231 preferably determines the presence or absence of correlation between plots for each repeated processing. This allows the processing to proceed while checking the validity of the electron density map for each repeated processing. As a result, efficient processing is possible when computational resources are limited.

[0037] When there is no correlation in the first plot, the trend analysis unit 232 performs a multivariate analysis on the distribution of the first plot. Examples of multivariate analysis include MCA (multiple correspondence analysis) and PCA (principal component analysis). This makes it possible to determine the presence or absence of some kind of trend even if there is no correlation. For example, even if there is no correlation in the entire data, by separating multiple types of correlated data, each type of data can be used as correlated data.

[0038] The theoretical size calculation unit 245 creates a second plot by plotting a parameter representing the molecular size calculated based on a plurality of electron density maps for each voxel size. The parameter representing the calculated molecular size is χ of the regression line of the calculated radius of gyration Rg(ind). 2 It is preferable to use the intercept Rg(sect) at = 1. Then, the theoretical size calculation unit 245 calculates a calculated value Rg(calc) of a parameter that represents the molecular size of a polymer in a solution independent of the voxel size, using the second plot.

[0039] The actual size calculation unit 246 calculates a parameter representing the molecular size of the polymer in the solution as an actual value from the measured X-ray scattering profile. Specifically, a Guinier plot is performed, and the actual value Rg(exp) of the dynamic radius of rotation of the molecule can be calculated. When the sample forms a hydration sphere in the solution, it is preferable to treat the numerical value obtained by subtracting a predetermined value for the hydration sphere from the numerical value obtained from the Guinier plot as the actual value Rg(exp).

[0040] The overall judgment unit 257 judges whether there is a statistically significant difference between the calculated value Rg(calc) of the radius of gyration calculated by the theoretical size calculation unit 245 and the actual measurement value Rg(exp) calculated by the actual size calculation unit 246. If it is judged that there is no significant difference, a representative electron density map is selected from the multiple electron density maps. If it is judged that there is a significant difference, the process is terminated.

[0041] The electron density map selection unit 258 selects a representative electron density map from the multiple electron density maps based on the calculated index. Specifically, the electron density map selection unit 258 selects a representative electron density map from the multiple electron density maps based on the Rg-χ2 correlation of the multiple electron density maps obtained, and based on the χ 2 The electron density map whose σ is close to 1 is selected as the representative electron density map. Since the representative electron density map is selected based on the index, the electron density map of a polymer in solution that has a dynamically fluctuating structure can be accurately reproduced. As a result, even biopolymers in solution with no prior information can be accurately visualized.

[0042] It is preferable that the electron density map selection unit 258 does not select a representative electron density map when there is no correlation in the first plot. This makes it possible to stop identifying electron density maps and omit unnecessary calculations when none of the electron density maps are valid. Then, it is possible to regenerate the electron density map or perform a re-experiment depending on the situation.

[0043] It is preferable that the electron density map selection unit 258 does not select a representative electron density map if the difference between the calculated value and the measured value is not within a predetermined range. This makes it possible to stop identifying an electron density map when the validity of the electron density map is not guaranteed in terms of molecular size, even if the electron density map can be identified.

[0044] [Electron density map identification method] (entire method) A method for identifying an electron density map of a polymer in a solution using the electron density map identifying system 10 configured as described above will be described. FIG. 4 is a flowchart showing the operation of the electron density map identifying device 200. First, the X-ray solution scattering device 100 sends a solution containing a sample S0 to a predetermined position and irradiates the sample S0 with X-rays. The X-ray solution scattering device 100 detects the scattered X-rays and transmits them to the computer 210 as X-ray scattering profile data. The computer 210 stores the received X-ray scattering profile data.

[0045] The computer 210 reads out data of an X-ray scattering profile obtained from a sample S0 for which an electron density map is to be specified in response to a user's designation (step S1). Then, the computer 210 acquires conditions for generating an electron density map, such as a boundary value size, a voxel size, and the number of trials for each voxel size, designated by the user (step S2).

[0046] An electron density map is generated from the read X-ray scattering profile in accordance with the acquired generation conditions (step S3). The generation of the electron density map will be described in detail later. Next, a theoretical scattering profile is calculated based on the generated electron density map (step S4). Based on the read measured X-ray scattering profile and the calculated theoretical scattering profile, a calculated value Rg(ind) of the particle gyration radius of the target molecule for each electron density map and an index χ representing the degree of agreement between the calculated X-ray scattering profile based on the electron density map and the measured X-ray scattering profile are calculated. 2 is calculated (step S5), and 2 A plot of -Rg(ind) is created (step S6).

[0047] Next, as a repetition condition, it is determined whether or not generation of an electron density map for a specific voxel size has been attempted a predetermined number of times (step S7). If it is determined that the predetermined number of attempts has not been made, the process returns to step S3. If it is determined that the predetermined number of attempts has been made, the process proceeds to step S8. The predetermined number of times is, for example, 50 times. Note that, although the process is repeated for a specific voxel size in step S7 in the above example, the process may simply be repeated a predetermined number of times.

[0048] The χ thus created for a particular voxel size 2 It is determined whether or not there is a correlation in the plot of -Rg(ind) (step S8). Details of the correlation determination process will be described later. If it is determined that there is no correlation, it is determined whether or not there is any trend in the plot by multivariate analysis (step S9). If it is determined that there is a trend, the process returns to step S3, the conditions are changed, and an electron density map is created again. If it is determined that there is no trend, the series of processes ends without selecting a representative electron density map. By determining whether or not there is a correlation at the stage where the repeated process of step S7 is completed and terminating processes that are unlikely to occur, computational resources can be used efficiently.

[0049] On the other hand, if it is determined in step S8 that there is a correlation, it is determined whether or not the condition for ending the repetition, that is, completing the generation of electron density maps for all of the multiple voxel sizes, is met (step S10). If it is determined that the condition is not met, the voxel size is changed and the process returns to step S3.

[0050] In step S10, when the condition for ending the repetition is met, χ 2 - Obtain a regression line from the plot of Rg(ind), and calculate the χ 2The intercept Rg(sect) at =1 is calculated (step S11). Then, a plot of the intercept Rg(sect) against the voxel size is created (step S12), a regression line is obtained from the plot, and the calculated value Rg(calc) of the radius of gyration of the molecule is calculated as an extrapolated value where the voxel size is zero on the regression line (step S13). Meanwhile, a Guinier plot is created for the read X-ray scattering profile, and the measured value Rg(exp) of the radius of gyration of the molecule is calculated (step S14).

[0051] Next, by determining whether the difference between the calculated radius of rotation Rg(calc) and the measured value Rg(exp) is within a certain range, it is determined whether the calculated value Rg(calc) is valid (step S15). At this time, if the sample forms a hydration sphere in the solution, it is preferable to treat the value obtained by subtracting a predetermined value for the hydration sphere from the value obtained from the Guinier plot as the measured value Rg(exp). If a hydration sphere is formed, the predetermined value is preferably 1.5 Å to 2.0 Å. Alternatively, the size of the hydration sphere estimated by various calculation methods aimed at explicitly calculating the existence of the hydration sphere may be used.

[0052] In step S15, if it is determined that the calculated value Rg(calc) is not valid, the series of processes is terminated without selecting a representative of the electron density map. If it is determined that the calculated value Rg(calc) is valid, the series of χ 2 From the electron density map according to the -Rg correlation, χ 2 A representative electron density map is selected from those for which is closest to 1, and the selected electron density map is output to the output device 290 (step S16), thus completing the series of processes.

[0053] The representative electron density map is not necessarily a single map, but may be multiple maps. For example, χ 2 -Rg(ind) plot shows a strong set of correlations and χ 2When multiple electron density maps are obtained in which α is extremely close to 1, these may be selected as the electron density maps corresponding to the respective canonical structures of the dynamic structure ensemble. In this case, it is preferable to select the correlation with the smallest voxel size. Alternatively, it is preferable to select the correlation defined with the smallest voxel size from among the correlations generated with various voxel sizes.

[0054] In the above example, multiple electron density maps are generated for each repetition, but they may be generated at once by parallel processing. Also, a certain number of parallel processes may be repeated. The choice of which process to use depends on which is more important: computational resources or the speed at which results are obtained.

[0055] (Generation of electron density maps) Next, the generation of the electron density map will be described in detail. Figure 5 is a graph showing an example of an X-ray solution scattering profile. When a biopolymer in a solution is irradiated with X-rays, the scattering rate is q≦0.7Å. -1 A gentle ring-shaped scattered X-ray intensity peak appears in the range of about 0.7Å. By integrating this in the circumferential direction, the X-ray solution scattering profile shown in Figure 5 is obtained. -1 By acquiring and analyzing scattering intensity data with high precision between and , it becomes possible to directly visualize electron density that is meaningful for the actual structure.

[0056] Figure 6 is a schematic diagram showing an electron density map. In generating an electron density map, the volume of a cubic box with side length H in real space containing the polymer is first discretized into an N×N×N grid of cubic voxels (N=4 in the example shown in Figure 6). As the shading of each voxel in Figure 6 indicates, the electron density ρ(x,y,z) of each voxel is given a random value within a certain range. Then, the three-dimensional reciprocal space intensity is calculated from the three-dimensional structure factor and divided into concentric shells as a function of the magnitude of the scattering vector q.

[0057] The 3D scattering intensities are then converted to 1D profiles and compared to the experimental scattering data. The 3D structure factors are scaled to match the experimental data for each q concentric shell, and a new electron density map is created in real space by inverse Fourier transformation. The density outside the map is set to zero. A new structure factor is obtained by forward Fourier transformation, and the cycle is repeated until convergence. A different electron density map is thus generated for each trial, and the index χ 2 and the calculated value Rg(ind) is calculated.

[0058] (Correlation determination process) The calculated χ for each electron density map 2 By plotting Rg(ind) and Rg(ind) and determining whether they are correlated with each other, the validity of the electron density map for the measured data can be determined. Whether the plot is correlated can be objectively determined, for example, by using a correlation coefficient. Furthermore, if there is no correlation, by determining whether the plot has a trend, it can be determined whether the data is unpromising or could be meaningful depending on the measurement conditions.

[0059] Figures 7(a) and 7(b) show the ideal distribution and the unanalyzable χ 2 7(a) is a graph showing the distribution of −Rg(ind). In the ideal distribution shown in FIG. 2 The plot of -Rg(ind) shows a correlation, which indicates that the multiple electron density maps are valid. On the other hand, in the unanalyzable distribution shown in Figure 7(b), the χ 2 The plot of -Rg(ind) shows no correlation or trend, indicating that the multiple electron density maps are invalid. 2 An electron density map whose σ is within a predetermined range from 1 can be selected as a representative electron density map.

[0060] [Example] An electron density map was actually determined using a sample of a biopolymer in solution (human serum albumin (HSA)). Electron density maps were generated by 50 trials for each voxel size of 10 Å, 5 Å, 4 Å, and 3 Å on a side. The chi-square of the generated electron density map was then calculated. 2 and Rg(ind) were calculated. 2 1 is a graph showing the distribution of the calculated molecular radius of gyration Rg(ind) versus voxel size of 10 Å, 5 Å, 4 Å, and 3 Å.

[0061] Then, based on the straight line representing the correlation, Rg(sect) was calculated for each of the voxel sizes of 10 Å, 5 Å, 4 Å, and 3 Å. FIG. 9 is a graph showing the extrapolation of Rg(sect) for the voxel size of the embodiment. The voxel size and the obtained Rg(sect) were plotted, and Rg(calc) for the entire multiple electron density maps was calculated. From these results, it was found that the generated electron density map was valid.

[0062] FIG. 10 is a list showing the electron density map and the processing results in the embodiment. Since a more appropriate electron density map can be obtained by reducing the voxel size, χ 2 According to the list obtained, χ 2 The electron density map of the 13th trial, in which the difference from 1 was 0.002, was the most appropriate, and was therefore selected as the representative electron density map.

[0063] 11(a) to 11(c) are front, top, and right side views, respectively, showing the selected electron density map. As described above, the electron density map in the 13th trial was identified and visualized with a voxel size of 3 Å.

[0064] The visualized electron density shows an overall shape similar to that of human liver. This well represents the molecular surface shape obtained from X-ray crystal structure analysis of HSA. Furthermore, in Figure 11(a), a depression of about 5 Å and a cylindrical bulge along it are observed from the center of the longest side at the bottom right to the top left. The visualized shape thus far matches well with the shape obtained from X-ray structure analysis not only in terms of the overall shape but also in terms of the fine features of the molecular surface structure. [Explanation of symbols]

[0065] 10. Electron Density Map Identification System 100 X-ray solution scattering device 110 X-ray generation section 111 X-ray source 115 Optical system 117 Cratsky Block 120 Sample Loading Mechanism 125 Sample holding tube 130 Detector 140 Control Unit 200 Electron density map identification device 210 Computer 211 Input / Output Control Unit 215 Measurement control section 217 Measurement data storage unit 221 Electron density map generator 225 Theoretical scattering intensity calculation section 226 Indicator calculation section 231 Correlation judgment unit 232 Trend Analysis Department 245 Theoretical Size Calculation Section 246 Actual size calculation section 257 General Judging Department 258 Electron density map selection section 280 Input Device 290 Output Device L Control bus

Claims

1. A radius of gyration calculation device for calculating the radius of gyration of a polymer in a solution, comprising: an electron density map generation unit that generates a plurality of electron density maps from an actually measured X-ray scattering profile obtained by measuring a sample; for each of a plurality of voxel sizes, a plot of the dynamic radius of gyration of the molecule calculated based on the plurality of electron density maps is created as a second plot, and an extrapolated value at which the voxel size becomes zero on the regression line of the second plot is calculated as the final calculated value of the dynamic radius of gyration of the molecule. A radius of gyration calculation device characterized by comprising a theoretical size calculation unit.

2. further comprising an index calculation unit that calculates an index representing the degree of coincidence between the calculated X-ray scattering profile calculated from each of the plurality of electron density maps and the actually measured X-ray scattering profile; The theoretical size calculation unit creates the second plot based on a first plot that is a plot of the dynamic radius of gyration of the molecule with respect to the calculated index created for each of the plurality of electron density maps. The radius of gyration calculation device according to claim 1.

3. For each of a plurality of voxel sizes, the dynamic radius of gyration of the molecule calculated based on the plurality of electron density maps is the intercept in the first plot. The radius of gyration calculation device according to claim 2.

4. an X-ray solution scattering device; a radius of gyration calculation device according to any one of claims 1 to 3, and the radius of gyration calculation device calculates the dynamic radius of gyration of the polymer in the solution based on the X-ray scattering profile of the polymer in the solution measured by the X-ray solution scattering device. A system characterized by this.

5. A radius of gyration calculation method for calculating a calculated value of the radius of gyration of a polymer in a solution, comprising: generating a plurality of electron density maps from an actually measured X-ray scattering profile obtained by measuring a sample; for each of a plurality of voxel sizes, creating a plot of the dynamic radius of gyration of the molecule calculated based on the plurality of electron density maps; calculating, as the final calculated value of the dynamic radius of gyration of the molecule, an extrapolated value at which the voxel size becomes zero on the regression line of the plot. A radius of gyration calculation method characterized by including steps.

6. A radius of gyration calculation program for calculating a calculated value of the radius of gyration of a polymer in a solution, A process of generating a plurality of electron density maps from an actually measured X-ray scattering profile obtained by measuring a sample, For each of a plurality of voxel sizes, a process of creating a plot of the dynamic radius of rotation of a molecule calculated based on the plurality of electron density maps, A rotation radius calculation program characterized by causing a computer to execute a process of calculating, as a final calculated value of the dynamic radius of rotation of the molecule, an extrapolated value at which the voxel size becomes zero using a regression line of the plot.

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