Introduction

The aim of this tutorial is to load the content of the log file, inoutput from SHELXC/D/E, in the workspace and create dataframes that canbe used for further analysis or data visualisation. Thecryfunctionread_SHELX_log can load in the R working memoryall the log files in output from SHELXC/D/E and give in output adataframe 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. Amongthem there are the SHELXC/D/E log files available with the currentrelease. To access the files, first load thecrypackage.

library(cry)library(ggplot2)

Next, have a look at what is included in the external-data directoryofcry.

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"           "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 examplebelow we show\(Chis ^2\) vs resolutionusing 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 functionread_SHELX_log when reading log files fromSHELXE five in output a list of dataframes. The user can choose the dataframe to use for further analysis.

## read the two hands log files separatelyfilename_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$CYCLEclass(cycle_i)

## [1] "data.frame"

names(cycle_i)

## [1] "wt"       "Contrast" "Connect"  "cycle"

FOM_mapCC_i<- obj_shelxe_i$FOM_mapCCclass(FOM_mapCC_i)

## [1] "data.frame"

names(FOM_mapCC_i)

## [1] "Res"   "FOM"   "mapCC" "N"

Site1_i<- obj_shelxe_i$Site1class(Site1_i)

## [1] "data.frame"

names(Site1_i)

## [1] "Site"    "x"       "y"       "z"       "occ.Z"   "density"

Site2_i<- obj_shelxe_i$Site2class(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$CYCLEclass(cycle_i)

## [1] "data.frame"

names(cycle_i)

## [1] "wt"       "Contrast" "Connect"  "cycle"

FOM_mapCC_0<- obj_shelxe_o$FOM_mapCCclass(FOM_mapCC_i)

## [1] "data.frame"

names(FOM_mapCC_i)

## [1] "Res"   "FOM"   "mapCC" "N"

Site1_o<- obj_shelxe_o$Site1class(Site1_i)

## [1] "data.frame"

names(Site1_i)

## [1] "Site"    "x"       "y"       "z"       "occ.Z"   "density"

Site2_o<- obj_shelxe_o$Site2class(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()