The Crown says Macdonald killed his brother-in-law after tensions over the future of the family farm they co-managed.
But his defence team says the problems on the farm had all been resolved and his killer remains a mystery.
The jury have heard more than three weeks of evidence and submissions from prosecution and defence lawyers, who gave their closing addresses last Friday.
The jury will resume their deliberations tomorrow morning.
Justice France told the jury it was agreed that whoever shot Mr Guy intended to kill him or knew it was likely.
But he warned the jury against thinking about the case as a murder mystery.
"Understandably, this case has been popularly described as a whodunit, but it's not.''
He urged the jury to put that to one side and said the case was an allegation that Macdonald killed Mr Guy.
Justice France said the jury had to be satisfied the prosecution had proved their case beyond reasonable doubt.
That meant the jury must be sure that Macdonald killed Mr Guy, rather than thinking it was likely or probable that he did.
The defence had floated alternatives to who may have killed Mr Guy, but those were "suggestions'' and were not matters the defence had to prove.
Macdonald was presumed to be innocent and he did not have to take the stand in the trial.
The jury could not give "any significance at all'' to his choice not to.
Justice France said Macdonald did not have to say anything before the trial but chose to when he was just a family member helping with the investigation.
That culminated with the police interview when the allegation of murder was put to him.
Justice France said it was a circumstantial case but many cases were, and there was nothing unusual about that.
"What it does mean though is that you need to be disciplined.''
Justice France said the prosecution was trying to establish various strands of facts. Any one on its own would not prove the case, but taken together they could.
He gave the alleged motive as an example, saying the jury had to consider whether the frustrations between Macdonald and Mr Guy in the months before the murder were still present.
"Was he still wound up about things, hostile to Kylee and Scott, or had he calmed down.''
Justice France said individual strands did not need to be proved beyond reasonable doubt, but a unanimous verdict was needed on the charge of murder.
He noted a majority verdict was possible, but the task for now was to reach a unanimous verdict.
He urged the jury not to be prejudiced or swayed by emotion, and to focus on the evidence.
Justice France said the focus in the jury room was not about providing closure for the family.
He said while jury members had probably admired the composure of Mr Guy's family as they gave evidence on the terrible circumstances, they had to focus on the evidence.
The jury had heard some unappealing things about Macdonald but could not leap from the conclusion that he had committed murder just because he had trashed a house being built on Scott and Kylee Guy's property.
"This isn't a trial about character,'' he said.
Justice France said Macdonald had lied about his past actions, but the jury could not conclude he lied about murder.
"You should not assume a lie is a sign of guilt.''
Justice France gave the jury directions on the forensic evidence of dive boot impressions at the scene.
The Crown alleges Macdonald wore Proline dive boots with a distinctive wavy pattern when he carried out the murder, but the defence said if a Proline boot was used at the scene, it was not in Macdonald's size.
Justice France said the jury should give weight to the evidence of an expert forensic witness, but the jury was also entitled to form an opinion on the boots based on the defence's argument.
Justice France said it was clear a dive boot had been used at the scene, but whether it was Proline boot or what size was worn was a matter for the jury.
The Crown alleges Macdonald may have used the farm shotgun to kill Mr Guy and there was no evidence of him having access to another shotgun.
Justice France said the real issue was whether Macdonald knew or might have known where the shotgun was stored in the farm office, which Mr Guy's father Bryan Guy had not told Macdonald.
In his closing, defence lawyer Greg King noted the risks involved had Macdonald murdered Mr Guy - the risk of being caught by his family, the risk of disposing of his equipment, the risk of detection and the risk of the consequences to his family.
The Crown argued Macdonald was able to carry out illegal acts without detection, as he had when he burned down an old house on the Guys' property.
In his closing, prosecutor Ben Vanderkolk said Macdonald had knowledge of the murder that only the killer had.
Justice France said the first contested issue was whether Macdonald knew Mr Guy had been shot before that was known to police. That came down to the evidence of witnesses at the scene.
The second issue was a phone call in which Macdonald said "his face'' to Bryan Guy when he called about Mr Guy's death. The Crown said it was significant because he would not have seen Mr Guy's face unless he was the shooter, while the defence said he was more likely to have said "his place''.
The prosecution argued Macdonald left offensive notes in the Guys' mailbox, which the defence denies.
Justice France said the Crown argued the notes straddled the two acts of damage - to an old farm house on the Guys' property and a new house being built there.
The defence argued the two rural post workers who claim to have seen the notes were hopelessly unreliable witnesses, and the notes did not come to light until much later.
Justice France said it was possible to view the arson and damage in two ways.
Mr King had argued they were acts of property but that was very different to killing someone. Macdonald reacted badly to Mr Guy's suggestion that he should inherit the family farm, but later made efforts to change.
Mr Vanderkolk had argued the arson and vandalism were personal acts stemming from a deeply embedded bitterness that was aimed at driving the Guys off the family farm.
Justice France said the jury could re-watch the police video interview with Macdonald if they needed to.
He urged them not to shrink from giving a verdict.
Earlier, the jury was told by Justice France Ewen Macdonald's murder trial is not a "whodunit'' but an allegation he killed Scott Guy that the Crown needs to prove beyond reasonable doubt.
The Crown alleges Macdonald shot and killed his brother-in-law Scott Guy, 31, at the end of the driveway of his Feilding home in the pre-dawn darkness of July 8, 2010.
Macdonald, 32, denies murder.
The Crown alleges Macdonald killed his brother-in-law after tensions over the future of the family farm they co-managed.
His defence team says the problems on the farm had all been resolved and his killer remains a mystery.
Justice France told the jury it was agreed that whoever shot Mr Guy intended to kill him or knew it was likely.
But he warned the jury against thinking about the case as a murder mystery.
"Understandably, this case has been popularly described as a whodunit, but it's not.''
He urged the jury to put that to one side and said the case was an allegation that Macdonald killed Mr Guy.
Justice France said the jury had to be satisfied the prosecution had proved their case beyond reasonable doubt.
That meant the jury must be sure that Macdonald killed Mr Guy, rather than thinking it was likely or probable that he did.
The defence had floated alternatives to who may have killed Mr Guy, but those were "suggestions'' and were not matters the defence had to prove.
Macdonald was presumed to be innocent and he did not have to take the stand in the trial.
The jury could not give "any significance at all'' to his choice not to.
Justice France said Macdonald did not have to say anything before the trial but chose to when he was just a family member helping with the investigation.
That culminated with the police interview when the allegation of murder was put to him.
Justice France said it was a circumstantial case but many cases were and there was nothing unusual about that.
"What it does mean though is that you need to be disciplined.''
Justice France said the prosecution was trying to establish various strands of facts. Any one on its own would not prove the case, but taken together they could.
He gave the alleged motive as an example, saying the jury had to consider whether the frustrations between Macdonald and Mr Guy in the months before the murder were still present.
"Was he still wound up about things, hostile to Kylee and Scott, or had he calmed down.''
Justice France said individual strands did not need to be proved beyond reasonable doubt, but a unanimous verdict was needed on the charge of murder.
He noted a majority verdict was possible, but the task for now was to reach a unanimous verdict.
He urged the jury not to be prejudiced or swayed by emotion, and to focus on the evidence.
Justice France said the focus in the jury room was not about providing closure for the family.
He said while the jury had probably admired the composure of Mr Guy's family as they gave evidence on the terrible circumstances, they had to focus on the evidence.
The jury had heard some unappealing things about Macdonald but the jury could not leap from the conclusion that he had committed murder just because he had trashed a house being built on Scott and Kylee Guy's property.
"This isn't a trial about character,'' he said.
Justice France said Macdonald had lied about his past actions, but the jury could not conclude he lied about murder.
"You should not assume a lie is a sign of guilt.''
