In 1946 van Arkel personally encouraged Clara to take up the study of X-ray crystallography, so that she could become his assistant. Dr. Ketelaar, who had been running the X-ray crystallography laboratory at Leiden, had recently left, and van Arkel asked Clara to take over his work. Van Arkel arranged for Clara to receive training in Amsterdam with Caroline MacGillavry, a highly skilled and recognized expert in the field of X-ray crystallography. Thus Clara continued her graduate studies working one day each week with MacGillavry in Amsterdam and the rest of the week working at the University of Leiden.
According to Clara, MacGillavry was a wonderful person with whom to work. MacGillavry was clearly a major influence on Clara's favorable introduction to this discipline. Although MacGillavry was employed as a reader at Amsterdam University at that time, eventually her work was so distinguished that a professorial position was created for her. She was active in the international world of X-ray crystallography and had many contacts in other countries.
From 1949 to 1954 Clara published scientific papers with her Dutch colleagues on the crystal structure of complexes of monovalent ions such as K2AgI3, K2CuCl3 and other isomorphous substances. These compounds were suggested for her study by van Arkel and the compounds were prepared for her in his laboratory. She took the X-ray crystallography data with the instrumentation at Leiden and then worked out the interpretations with MacGillavry's help in Amsterdam.
When Clara completed her Ph.D. degree in 1950 she began working full-time as an X-ray crystallographer for van Arkel at Leiden. She published papers with van Arkel and other members of the Chemistry Department at Leiden both before and after she came back from working with Dorothy Hodgkin in 1950-51. However, she felt that her facilities were inadequate and even hazardous due to the location of her office desk in the same room with the X-ray equipment. Originally she worked on the third floor with a dark room in the basement, but eventually she moved into a larger space that was still without a separate office area. She felt that it was hazardous to have her desk and darkroom facilities all in the same room with X-ray equipment that would run for hours at a time.
In fact she was so unhappy with her situation that Caroline MacGillavry suggested she go abroad to study compounds outside the group of inorganics that she had worked on for her Ph.D. degree. MacGillavry helped her obtain funding through a one-year fellowship from the International Federation of University Women and in 1950 Clara went "abroad" to study at Dorothy Hodgkin's laboratory in Oxford, England.