Read SHELXC/D/E log file • cry

Introduction

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 read_SHELX_log 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.

Sample SHELXC/D/E log files.

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)
library(ggplot2)

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_phases.mtz"           "1dei-sf.cif"              
##  [3] "2ol9_phases.mtz"           "3syu.cif"                 
##  [5] "6vww_xds_ascii_merged.hkl" "AMS_DATA.cif"             
##  [7] "e-65-00i60-Isup2.rtv"      "shelxc.log"               
##  [9] "shelxd.log"                "shelxe_i.log"             
## [11] "shelxe_o.log"              "xds00_ascii.hkl"

SHELXC

Let start to have look at SHELXC log file.

filename <- file.path(datadir,"shelxc.log")
obj_shelxc <- read_SHELX_log(filename)
class(obj_shelxc)

## [1] "data.frame"

names(obj_shelxc)

## [1] "Res"      "N_data"   "Chi_sq"   "I_sig"    "Complete" "d_sig"    "CC1_2"

Using cry we plot all the classic charts of SHELXC. In the example below we show \(Chis ^2\) vs resolution using the functionplot_SHELX.

plot_SHELX(obj_shelxc, var = obj_shelxc$Chi_sq, type = "shelxc",
           title_chart = "Chis ^2") +
  theme_cry()

SHELXD

filename <- file.path(datadir,"shelxd.log")
obj_shelxd <- read_SHELX_log(filename)
class(obj_shelxd)

## [1] "data.frame"

names(obj_shelxd)

## [1] "CCall"  "CCweak"

Plot CCall vs CCweak using ggplot2

plot_SHELX(filename = obj_shelxd, type = "shelxd") +
  theme_cry()

SHELXE

The function read_SHELX_log 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 <- read_SHELX_log(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 <- read_SHELX_log(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"

Plot inverted and original hand.

plot_SHELX(filename = obj_shelxe_i, filename_e = obj_shelxe_o,
           type = "shelxe") +
  theme_cry()