The aim of this tutorial is to load the content of the log file, in output from SHELXC/D/E, in the workspace and create dataframes that can be used for further analysis or data visualisation. The cry function readSHELXlog can load in the R working memory all the log files in output from SHELXC/D/E and give in output a dataframe for SHELXC/D and a list of dataframes for SHELXE.
Some sample files are stored as external data in this package. Among them there are the SHELXC/D/E log files available with the current release. To access the files, first load the cry package.
library(cry)Next, have a look at what is included in the external-data directory of cry.
datadir <- system.file("extdata",package="cry")
all_files <- list.files(datadir)
print(all_files)## [1] "1dei-sf.cif" "1dei_phases.mtz"
## [3] "2ol9_phases.mtz" "6vww_xds_ascii_merged.hkl"
## [5] "AMS_DATA.cif" "e-65-00i60-Isup2.rtv"
## [7] "shelxc.log" "shelxd.log"
## [9] "shelxe_i.log" "shelxe_o.log"
## [11] "xds00_ascii.hkl"
Let start to have look at SHELXC log file.
filename <- file.path(datadir,"shelxc.log")
obj_shelxc <- readSHELXlog(filename)
class(obj_shelxc)## [1] "data.frame"
names(obj_shelxc)## [1] "Res" "N_data" "Chi_sq" "I_sig" "Complete" "d_sig" "CC1_2"
Plot \(Delta*F/sig(Delta*F)\) vs resolution.
library(ggplot2)
ggplot(obj_shelxc, aes(1/(Res)^2, d_sig)) +
geom_point() + geom_line() + theme_bw() +
xlab(expression(h^2 * (ring(A)^-2))) +
ylab(expression(Delta*F/sig(Delta*F)))filename <- file.path(datadir,"shelxd.log")
obj_shelxd <- readSHELXlog(filename)
class(obj_shelxd)## [1] "data.frame"
names(obj_shelxd)## [1] "CCall" "CCweak"
Plot CCall vs CCweak using ggplot2
library(ggplot2)
ggplot(obj_shelxd, aes(CCall, CCweak)) +
geom_point() + theme_bw() +
xlab('CCall') + ylab('CCweak') The function readSHELXlog when reading log files from SHELXE five in output a list of dataframes. The user can choose the data frame to use for further analysis.
## read the two hands log files separately
filename_i <- file.path(datadir,"shelxe_i.log")
obj_shelxe_i <- readSHELXlog(filename_i)
class(obj_shelxe_i)## [1] "list"
names(obj_shelxe_i)## [1] "CYCLE" "FOM_mapCC" "Site1" "Site2"
cycle_i <- obj_shelxe_i$CYCLE
class(cycle_i)## [1] "data.frame"
names(cycle_i)## [1] "wt" "Contrast" "Connect" "cycle"
FOM_mapCC_i <- obj_shelxe_i$FOM_mapCC
class(FOM_mapCC_i)## [1] "data.frame"
names(FOM_mapCC_i)## [1] "Res" "FOM" "mapCC" "N"
Site1_i <- obj_shelxe_i$Site1
class(Site1_i)## [1] "data.frame"
names(Site1_i)## [1] "Site" "x" "y" "z" "occ.Z" "density"
Site2_i <- obj_shelxe_i$Site2
class(Site2_i)## [1] "data.frame"
names(Site2_i)## [1] "Site" "x" "y" "z" "h.sig." "near" "old" "near.1"
## [9] "new"
filename_o <- file.path(datadir,"shelxe_o.log")
obj_shelxe_o <- readSHELXlog(filename_o)
class(obj_shelxe_o)## [1] "list"
names(obj_shelxe_o)## [1] "CYCLE" "FOM_mapCC" "Site1" "Site2"
cycle_o <- obj_shelxe_o$CYCLE
class(cycle_i)## [1] "data.frame"
names(cycle_i)## [1] "wt" "Contrast" "Connect" "cycle"
FOM_mapCC_0 <- obj_shelxe_o$FOM_mapCC
class(FOM_mapCC_i)## [1] "data.frame"
names(FOM_mapCC_i)## [1] "Res" "FOM" "mapCC" "N"
Site1_o <- obj_shelxe_o$Site1
class(Site1_i)## [1] "data.frame"
names(Site1_i)## [1] "Site" "x" "y" "z" "occ.Z" "density"
Site2_o <- obj_shelxe_o$Site2
class(Site2_i)## [1] "data.frame"
names(Site2_i)## [1] "Site" "x" "y" "z" "h.sig." "near" "old" "near.1"
## [9] "new"